The South Korean version of the game (released two years after the original Japanese edition) contains eleven unused maps not found in any other release, featuring fully 3D environments which do not line up with any locations present in the finished product. All assets related to these maps are dated after the game's Japanese release, with intervals ranging from five days to just over three months. Additionally, the maps' texture names are written in Romanized Japanese rather than Korean, indicating that they were not created by Nintendo of Korea.

Two of these maps, kri_04 and kri_05, additionally feature various cat NPCs, all drawn in substantially different art styles compared to not only each other, but also the final game. Each one is named after a developer from the Super Paper Mario staff: yamada_neko02 (Koichiro Yamada), koba_neko (Sayuri Kobayashi), tuka_neko (Naoko Tsukamoto), and kawa_neko (Chie Kawabe).

Of these four, kawa_neko is the most unique, and was apparently designed as a player character. Firstly, the cat's name is only given to its mesh, with its sprite instead being named bc_all.1. Additionally, kawa_neko features an animated tail and a mesh that is centered on the ground rather than the middle of the room. Furthermore, new_neko_18, a redesigned version of kawa_neko with white fur instead of black, can be found in kri_08, kri_09, and kri_10; new_neko_18's mesh is explicitly labeled "PLAYER" in the data for these maps.

Taken together, all of these elements imply that these early rooms were created as a proof-of-concept for an original project by Intelligent Systems that ended up cancelled for unknown reasons.

In Chapter 2-3: Breaking the Bank, it is possible to work off your debt of one million Rubees without finding Slim and stealing the needed currency from the mansion's vault. Although there are no differences in the stage's ending if you do this, working off the debt acts as a lengthy sequence break as traveling back to the vault after working and paying off the full debt will reveal that the counter on the vault door now displays 0, and the vault can be opened freely without entering the password to reveal that it is empty.

On the other hand, manually working to collect over 9,999,999 Rubees will result in the Rubees counter in the HUD overflowing and appearing to start back at 0 due to it only displaying seven digits, but in reality the game does register the collection of more than ten million Rubees and allows you to complete the level.

Six months after the American release of Super Paper Mario, American film director, producer, and screenwriter Seth Gordon, who's most recent works include the Pixels movie, had interest adapting a movie based on Super Paper Mario. Gordon was quoted saying, "I'd love, really love, to adapt Super Paper Mario into a movie, a movie that would constantly switch from 2D to 3D. In five years, 3D cinema is going to be really big." Gordon however specified that he never had the chance to speak with Nintendo about his envisioned project, so his idea was eventually forgotten.

The Underchomp is based on the legendary hell-hound Cerberus, a giant three-headed dog who guarded the gates of Hades in Greek mythology. In one story, he was put to sleep by the music of Orpheus, which inspired Piccolo's music putting the Underchomp to sleep.

A Gold Fuzzy makes an appearance on the back cover of the game's official guidebook, but no Gold Fuzzies appear in-game.

In the game's coding, there are a total of 9 unused enemies, some of which were present in the first Paper Mario game.

In the German version of the game, Francis the chameleon is named Konrad, a pun on Conrad, which is a popular German PC store.

There are six unused audio tracks in Super Paper Mario. The first one is named "Dummy_32k". Dummy plays the tune of World 1-1 from "Super Mario Bros 3." Another is named "b_happy_flower_44k_lp." It's name suggests it was going to be used for when Mario uses the Happy Flower item. The next audio track is called "evt_relax1_44k_lp." This track is a peaceful, relaxing tune. It might been planned for use near the end of the game. The 4th audio track is called "evt_stg3_open1_44k_lp." It was most likely going to be used for a opening of a level in World 3. The next is called "ff_corrrect2_e3_32k." This unused jingle's name suggests there was supposed to be more than one jingle. The final unused audio track is a jingle named "ff_fault1_32k." This was most likely going to be used when failing a Mini-game.

Super Paper Mario was originally going to be released exclusively for the Nintendo GameCube before being moved to the Wii. Evidence exists on the game's data, as there is a folder which contains GameCube rendered models of characters like Mario and Princess Peach. The Wii textures are about 50% larger.

There's an unused enemy in the game's data named "Fly Guy" which is a Flying Shy Guy using a propeller. It's unknown where this would have been used in the game.

In both of Francis' rooms where he keeps his keys, there are references to previous Paper Mario games. Bow the Boo and her butler, Bootler, are found on a poster along with Petuni, who also appears as a plushy with Punio, Vivian, the Yoshi Kid in all colors, Peach, various items, and Pennington. The left most room also contans a famicom/NES, a SNES, a Virtual Boy, a Nintendo 64, and a Gamecube.

Near the end of the game, Dimentio will ask you to join his side to take down Count Bleck. If you say yes four times, he will enslave the characters and you will get a game over.

The enemy Fracktail makes a reference to Zelda II: The Adventure of Link. When Dimentio causes Fracktail to short circuit, he says "I am Error", one of the NPCs in Mido Town.

It is possible to get a game over at the beginning of chapter 4-1. After getting the helmet go into the door. When it asks you if you want to put on the helmet, say no. Do this until Tippi says "If you don't, do you have any idea what your fate will be? AWFUL. Do you want this?" Answer yes to every question after this. After this Tippi will leave and you will get a Game Over.

Near the beginning of the game, Merlin tells you to take the pure heart and save all worlds from destruction. If you say no three times, you'll get a game over.

An early, unused title screen can be found in the game's files. The copyright date is listed as 2006 instead of 2007, and in Thoreau's place is a Pixl who resembles a ladder which was not included in the final game. The Pixl also appears in a pre-release screenshot of the battle against Big Blooper.

There was one change to the game's script between the two English localizations. In North America, Dimentio insults Luigi by calling his mustache a "shag", but as this doubles as a vulgar slang term in British English (a reference to the act of sex), it was changed to "pushover" in the PAL region.