Within the data for Chapter 2 is a placeholder graphic for Queen's arcade cabinet that depicts it with green paneling and the word "Xbox" crudely written on the marquee. Despite the fact that it was never intended to be featured in the normal course of play, the sprite was altered in the version 1.06 update to remove the "XBOX" text, presumably to avoid potential trademark issues.

In Spoiler:the Weird Route version of Chapter 4, one pivotal scene depicts Spoiler:Kris, possessed by the SOUL, forcing Noelle to re-don the Thorn Ring from Chapter 2 by slowly creeping towards her as she backs away in fear across a couch. In the original release of the chapter, this gives way to an animation Spoiler:of a rose blooming and then crumbling against a black screen, located in the same place as Noelle's sprite. In the Version 1.01A update, this was replaced by Spoiler:a single red pixel, possibly as a placeholder graphic, which in turn was replaced in Version 1.01C with another animation depicting cracking red glass. The original animation is outright removed from the game's files in these later updates rather than being merely disabled.

The reason for this alteration was not explained in the official changelogs, which vaguely described the changes as a "Small graphical alteration to a certain scene" and "Strengthened imagery while maintaining a scene's intended meaning". The animation changes were likely made initially in response to complaints and discussion among players who misinterpreted the scene as Spoiler:Noelle being forcibly "deflowered" (taking her virginity, in this case through rape) literally, in addition to being driven insane, and then to counter-complaints Spoiler:lamenting the reduced impact when the single red pixel was implemented.

Both earlier revisions of this sequence are referenced if the player continues the Weird Route into Chapter 5. Spoiler:The chapter's opening cutscene on the route depicts the same red pixel as the Version 1.01A rendition, after which Noelle is heard echoing her line, "thank you," which follows the Thorn Ring sequence in Chapter 4. If the player aborts the route during the lake scene, Kris' title is changed to "Shattered Rose," with the accompanying description reading "Only one knows the rose's meaning." While not the only "rose" title in Chapter 5, the specific use of the descriptor "shattered" aligns with the crumbling animation from Chapter 4's initial release.

Within the data for Chapter 4 are unused sprites depicting Susie playing a handheld video game while hanging out with Noelle. Concept art for this was shown off in a tweet by Toby Fox in 2022, alongside artwork of two other character interactions. Notably, the Susie and Noelle scenario is the only one shown in the tweet that isn't featured in the final game.

In the original release of Chapter 4, Susie's response to Catty drinking a bowl of milk in Hometown's alleyway read "(That's MY free milk, you furry degenerate...)". In the Version 1.01B update, this line was slightly rewritten to instead have Susie call Catty a "furry freak." No explanation was given for this change in the official changelog, which does not mention it whatsoever.

Within the data for Chapters 3 and 4 is an unused chart editor for Lightners Live, the rhythm minigame in Chapter 3. This editor, which can be accessed via debug mode, is fully functional and supports the ability to create, save, and load beatmaps. The pre-loaded charts include both songs found in the final game as well as unused ones: "Doom Board", "Ruder Buster", "Vapor Buster", "Rude Buster", "Field of Hopes and Dreams", and "tenna_battle_old" (a duplicate of "It's TV Time!" with an earlier ending). Furthermore, the editor's chart for "It's TV Time!" is substantially longer than the one used in Tenna's boss fight. The charts additionally feature different names compared to the versions in the chapters' soundtrack albums, such as "MIKE, The BOARD, please!" being called "How To Play" and the Chapter 3 version of "Raise Up Your Bat" being called "Lightners Live".

Within the game's data is an unused "Talk" button for the Dark World's overworld menu, intended to allow the player to hear observations from Kris' party about the current area, similarly to the tattle feature in the Paper Mario series. The game's code still contains a script, scr_talkroom, which points to this scrapped dialogue, though the only remaining text is a single placeholder line: "Your voice echoes aimlessly." The Talk button also still has an icon and associated code placing it in the center of the menu, although the released game is programmed to omit it from display.

In a retrospective post detailing the making of Chapters 3 & 4, director Toby Fox revealed that the layout of Chapter 3 underwent multiple revisions over the course of development. Fox initially started with eight different segments (four boards and four minigames) which then expanded to 17 with the inclusion of additional rooms and interludes. The final game would trim it down to 12, with the third envisioned board (which would've featured a "city" theme) being removed entirely due to it not working with the game's overall style. Vestigial remnants of this axed board remain in Spoiler:the Sword Route, where a stripped down version of it appears near the end of the Original Game. A cowboy-themed minigame also ended up removed, with the final game distilling it heavily to a shooting gallery. According to Fox, this fluctuating approach was due to him wanting to keep Chapter 3's pacing from getting bogged down while still retaining the original idea of it being a homage to the Mario Party series and the Strange Fortress stage in Gunstar Heroes.

The various changes made to Chapter 3's layout are reflected in unused content left behind in the game's data. Among other things, the game's code still contains assets from the full version of Board 3, early versions of other boards and rooms, and corresponding unused dialogue, music, and graphics. The latter categories include both early versions of material found in the final game and assets that were removed altogether.

In early 2026, complaints arose from Latin American fans regarding the lack of official Spanish and Portuguese localizations of Undertale and Deltarune. This stemmed from earlier complaints over merchandise producer Fangamer's high shipping costs to Latin American countries, and a lack of South American tour dates for the "Undertale: The Determination Symphony" concert tour, both due to financial and logistical issues on part of Fangamer and the concert organizers.

In response, creator Toby Fox released a statement explaining that the reason why the games' only official translations were in English and Japanese was because he wanted to provide direct oversight to localizers in languages he was already fluent in. Since the games' scripts rely heavily on wordplay, he wanted the translations to adhere as closely as possible to his intended vision to reduce the risk of translation errors, adding that he was "not against official translations for other languages if we could make it work the same way..." Regarding Deltarune specifically, Fox expressed concerns that producing more translations would prolong the game's already drawn-out development, and endorsed unofficial fan translations as a way to allow fans to "interpret the game without the burden of being "officially" perfect". This statement drew mixed responses on social media, with some defending his perfectionist creative vision and efforts to manage the scope of development, while others felt that his standards were unnecessarily high and that the financial success of the games justified the demand for more translations.

From Chapter 2 onwards, the game's title screen includes a small subtitle below the main logo listing the current chapter. In addition to including graphics for Chapters 2 through 7 (lining up with the visible options on the chapter select screen), the game's data also includes Spoiler:graphics for Chapters 0, 1, 8, 9, and 10. While the Chapter 1 graphic is presumably for organizational purposes, the role of the remaining unused graphics is more ambiguous. As the game states that "THE HALFWAY MARK HAS BEEN ATTAINED" after completing Chapter 4, it is unclear whether the references to Chapters 0, 8, 9, and 10 were reflective of an earlier, longer outline for the game's story or if they were included as red herrings.

During the final battle of Chapter 3, Spoiler:the Roaring Knight is able to render Susie and Ralsei's HP to -999 when knocking them out, with the results represented by red text reading "SWOON". This appears to reference the Black Sword weapon in Final Fantasy IV, which has a chance of knocking out enemies in one hit. In the English localization of that game, the text "Swoon!" shows up when this occurs. The Knight further references this phenomenon with its own sword, the Black Knife (which also serves as its battle theme's namesake).

In a retrospective article detailing the making of Chapter 5, developer Toby Fox revealed that Seth was originally designed with lavender skin and white hair. The decision to revise this idea came about after his friends pointed out their resemblance to the character Amethyst from the 2013 American animated series Steven Universe. Concept art featured in the article showcases an early alternate design that features a uniformly white appearance barring a purple flower collar and a purple crescent moon decal on Seth's robe. A second design depicted in the same art features the same purple palette depicted in the final game, but retains the collar. While Seth's final design drops the decal and replaces their collar with a tie, the sprite based on the white design's pose features the tie curving into a crescent shape, alluding to this early idea.

Chapter 5 features many references and similarities to the Touhou Project series, of which developer Toby Fox and illustrator Temmie Chang are fans, through outfits, items, character designs, in-game text, and music. These include, but are not limited to, the following:

• The Red Ribbon and Netskie Hat headgears are references to Reimu Hakurei and Ran Yakumo.
• Aqua's character design, which Fox admitted was directly inspired by the Touhou series, bears similarities to characters such as Cirno, Sakuya Izayoi, and Koishi Komeiji.
• Flowery's line "Star sign: the Flower", presented like a dating simulator profile, is formatted similarly to Spell Cards' names, while bullet patterns throughout the chapter resemble Spell Card patterns.
• In the Ideal Diner, a Floradinn repeatedly orders eggs with increasingly hardening yolks, referencing difficulty options and stages in the Touhou games.
• The sound effect for collecting Flowery Dollar coins is a whispered voice resembling the graze sound effect from the licensed fangame Touhou Luna Nights.
• The Phanta item's description calls it a "grape-flavored phantasmagoria of a soda's dream", referencing Touhou Yumejikuu: Phantasmagoria of Dim. Dream. Its drink dispenser description, "Purple soda in hidden flavor", and ability to grant 16 TP allude to the 16th mainline game in the Touhou Project series, Touhou Tenkuushou: Hidden Star in Four Seasons.
• In Yellow's first punishment room, the party can encounter Shinobeetles trapped in quicksand asking "(Won't somebody please help me?)". This references a 2014 tweet by Fox about a presentation slide in a class lecture featuring a photoshop edit of Sakuya sinking in quicksand.
• The chapter's soundtrack quotes several Touhou themes, including "Theme of Eastern Story", "Lovely Mound of Cherry Blossoms ~ Japanese Flower", and "The Doll Maker of Bucharest". "Petal Dance," the battle theme for most of the colored flowers, prominently features Romantic Tp, a trumpet soundfont commonly used in the Touhou games and nicknamed the "ZUNpet" by fans. The "Shop 3" theme mimics the sound chip featured in the PC-9800 Touhou games.
• There are two references exclusive to the Japanese version of the game. Bullet patterns are referred to as "Danmaku", a term used for them throughout the Touhou series, while Flowery's "smile again" voice clip references a similar line from the Touhou fan video "My Name is Hong Meiling".

The BromideF and BromideR items reference the collectable bromides from the Lunar series of RPGs, which similarly feature high-quality illustrations of the games' cast members that pan up and down with warm background music. The BromideF illustration (depicting Flowery in a bubble bath) further parodies Borgan's Bromide and Lemina's Bromide 4 from Lunar 2: Eternal Blue Complete. All three illustrations feature the same poses, settings, and composition, but Flowery is fully clothed in BromideF.

In Chapter 3, if the player enters Mancountry, the hidden area containing that chapter's egg room, and looks through the binoculars on the western peninsula, they'll see a field of gray grass. Later, in the Weird Route version of Chapter 5, Spoiler:Kris receives a loaf of bread from Sans as a key item, with its Check description mentioning its tendency to leave crumbs everywhere. Both of these reference a glitch observed in the original 1989 Famicom release of EarthBound Beginnings, which exploits a quirk of the Bread Crumbs item (in which creating it for the first time in a playthrough with Pippi, returning her home, and then reclaiming her inventory resets its warp coordinates to [0, 0]) in order to transport the player to an out-of-bounds area consisting of monochrome graphics pulled from the last area they were in. Most users of this glitch trigger the bugged Bread Crumbs in Podunk, with the view from Mancountry's binoculars being identical to the consequent out-of-bounds area. These allusions to the glitch foreshadow Spoiler:the climax of Chapter 5's Weird Route, in which Noelle and the SOUL forcibly drag her and Kris through Hometown's lake, apparently going out of bounds as a result.

In Chapter 3, inputting exactly 1225 points into the giant gachapon machine in the B-Rank room unlocks a hidden door inside the front of the machine leading to gacharoom_unknown, a large maze of red carpet against a scrolling blue checkerboard background. The maze has no collision data and loops indefinitely, but one pathway eventually leads to a smaller gachapon machine. Interacting with this results in Kris acquiring a capsule containing a "small, dark triangle", hard like lacquer, that they then lose before becoming unable to find their own hand. Kris is then teleported back to the B-Rank room, and the giant gachapon machine is permanently removed. The background music for this area, labeled "findher" in the game's files, was previously featured in a hidden page in the Spamton Sweepstakes website, where it plays upon clicking an image of Dess' guitar.

When presenting Spoiler:Spamton NEO's Shadow Crystal to Seam at the end of Chapter 2, Seam states that Kris, Susie, and Ralsei will be unable to defeat their next opponent without the aid of the Shadow Mantle. In Chapter 3, the item appears as a hidden piece of armor obtained after Spoiler:completing the Sword Route, and, true to Seam's word, it significantly aids the player's chances of defeating Spoiler:the Roaring Knight by increasing the wearer's resistance to Dark and Star element attacks. Despite this, it is fully possible to defeat the boss without equipping the Shadow Mantle. Doing so and then obtaining the resultant Shadow Crystal results in unique dialogue from Seam when it is presented to them at the start of Chapter 4, in which they express their astonishment at the party's feat.

At the end of Spoiler:the Sword Route in Chapter 3, Spoiler: when Susie comes to greet Kris after the latter obtains the Shadow Mantle, the player is secretly given control of HERO_SWORD again. Consequently, it's possible to guide them back into the room and to Kris and Susie, which Kris notices. Attempting to attack Susie during this results in Kris pulling her away to protect her, whereupon she lets them taste her hair as compensation for her drinking their shampoo. Afterwards, Susie's dialogue proceeds as normal.

Two tracks in Deltarune prominently interpolate "Merry CD", a track that developer Toby Fox contributed to the Omori soundtrack. The first is "d", which plays during the cutscene that precedes Spoiler:the Weird Route version of the first Berdly fight in Chapter 2. The second is "Gingerbread House", the theme that plays inside the Holiday family's mansion in Chapter 4. The choice of reference alludes to how both sequences prominently focus on Noelle, matching the holiday theming of the Omori song.

Within the files for Chapter 5 is an early draft of Noelle's portraits for Spoiler:the drowning sequence at the climax of the Weird Route. While most of these portraits feature slightly more pixel padding than their equivalents in the final game, the last four are substantially different in design. Additionally, the last two depict Noelle Spoiler:continuing to fade into the black background rather than cutting to a frame of her shouting euphorically. Additionally, the final versions of these portraits feature an unused final frame depicting Spoiler:a close-up of Noelle's eyes, likely intended for her final line of dialogue (which, in the released game, instead duplicates the shouting frame from the previous line).

In a retrospective article detailing the making of Chapter 5, developer Toby Fox explained that the chapter's platforming mechanics were conceived shortly after Chapter 2's release in 2021, and were developed as a prototype before expanding in scope late into Chapter 4's development. According to Fox, a major issue with the mechanic's development was allowing it to mesh properly with the standard RPG gameplay of Deltarune, resulting in the formation of the ACT system and the addition of dialogue and RPG-style encounters in these sequences. The ACTs themselves originally encompassed a broad range of ideas before being whittled down to using Susie's Rude Buster and Ralsei's hanging ability. Fox also stated that the developers had to consider the possibility of Deltarune being many players' first experience with platforming gameplay, especially since Chapter 5, a relatively late point in the story, would be the first time it would appear in the game. Consequently, the level design was simplified to keep the "actual jumping challenges" from becoming too intense barring a few optional areas.