When deciding what characters would appear in the game, Nintendo EPD took inspiration from the original Donkey Kong arcade game, which established that Donkey Kong lived alongside humans. While the team debated how much human-related content and Donkey Kong Country-inspired elements would be included, producer Kenta Motokura mandated that the character Cranky Kong should appear because he was a fan of the character.

It was decided early on that another character would accompany Donkey Kong throughout the game, though no specific character had been included in the software design description. One developer suggested Pauline, with this idea being revisited following the implementation of Donkey Kong's "Zebra Bananza" form. The composer had written music for the transformation sequence, and the team decided to turn it into a song that Pauline could perform, having been established as a singer in Super Mario Odyssey. Both Motokura and director Kazuya Takahashi credited Pauline's inclusion with helping many of their ideas take form.

The Asian version of the Genesis port removes the MVS difficulty setting and replaces it with a Sound Test mode.

The character select backgrounds are different between the American and Asian versions of the Genesis port. The background is blue in the US version, while the Asian version has a black background along with the World Heroes logo.

A recurring oddity in the Pokémon games is that the Gym Leader and later Elite Four member Koga, the Kanto Region's Poison-type expert, threatens to defeat his opponents with both Poison and Sleep tactics. In Red and Blue, he states:


In Gold, Silver, Crystal, and their remakes HeartGold and SoulSilver, he states:


In FireRed and LeafGreen, he states:


Despite this, the only game in the series where Koga's main team uses any Sleep-inducing moves is Yellow, where two of his Venonats have Sleep Powder. In contrast, all of Koga's teams have incorporated Poisoning moves, with some of his teams being entirely composed of Pokémon using such moves. Although possibly a mistake, this might also tie into the theme of misdirection, which would be fitting for the ninja-themed Fuchsia Gym.

According to an animation reel from Neil Wrischnik, the Blocker Birds seen in The Phoenix Psanctuary were originally going to be enemies rather than NPCs, complete with unused animations and an unused trapping sequence suggesting that one of them was intended to appear as a playable villain character.

The "starburst effect" that occurs when bouncing on enemies is usually meant to expand, but in the first two Donkey Kong Country games, they were mistakenly coded to contract instead. This issue was fixed in the third game and the subsequent re-releases of all three games on the Game Boy Advance.

The developers of Crash Team Racing Nitro-Fueled were informed ahead of time that the game's post-launch support would be limited. Very little content was thought of, and none was worked on, for grands prix that didn't make it to release. Creative director Thomas Wilson stated the only scrapped grand prix concept he recalls is "Heroes vs. Villains", a superhero parody grand prix compared to the animated film Megamind, which would have featured a course in a "retro-futuristic" city and superhero and supervillain outfits for the racers.

Contrary to popular belief, there is no evidence that Mega Man 5 was banned or failed to release in Vietnam specifically because of Napalm Man's design, the similarities that his stage's design bears to areas within the country (including the Viet Cong's tunnel system used during the Vietnam War), or one of its enemies resembling a tiger species endemic to Vietnam among other similarities. The history of the Vietnamese video game market itself is poorly documented. It is currently believed that all video game imports were virtually banned by the Vietnamese government as a result of Cold War tensions until the implementation of the Đổi Mới reforms started in 1986, which allowed for some second-hand game console imports and rental arcades to pop up. They are thought to have become a more widely available commodity in the country in 1994, two years after Mega Man 5's release, when the United States lifted its 30-year-long trade embargo on Vietnam. There is no known documented information available on if there even was a Vietnamese reaction to Napalm Man at the time.

A short test map exists within the game that can only be accessed via an Action Replay cart. The map itself is a closed off room containing a series of platforms, Sabre Wulf, the treasure he guards, and a single power up. As the room itself has no exit, it is impossible to escape Sabre Wulf once Sabreman picks up the treasure.

Originally, Boggy's three children (Groggy, Soggy and Moggy) were intended to appear in the game as part of a challenge called "Don't Bring Your Kids to Work Day", but the challenge was scrapped due to time constraints. In 2019, it was discovered that Soggy and Moggy not only had fully completed models in the game, but also AI that was reused from the Minjos in the game. They can appear in Banjoland Act 6 during the challenge "Home Improvements: Igloo Edition", where Soggy can be found running on top of Clanker, while Moggy can be found running on top of the display case, both far away from where the actual challenge takes place. It is currently unknown if Groggy is anywhere in the game.

In addition to the console Anniversary Collection, a Game Boy Advance counterpart was also planned. Originally named Mega Man Mania, the title would have included colored remakes of the five Mega Man games created for the Game Boy, along with a History section and artwork. The compilation was planned for a Q4 2004 release, but was repeatedly delayed, partly due to Capcom reportedly having difficulty in locating the source codes for most of the games, forcing them to recreate them from scratch. In January 2006, it was announced the compilation was being "placed on indefinite hold" as Capcom and gaming retailers began issuing pre-order refunds.

Following the game's release in 2013, it was featured on the "Clueless Gamer" segment on comedian Conan O'Brien's Conan talk show. During this segment, O'Brien was able to play as Superman with the "Flaming C" costume. "Flaming C" was a character co-created by O'Brien and DC Comics artist Bruce Timm, modeled loosely on O'Brien himself. When asked about the Flaming C skin in 2021, game director Ed Boon confirmed that a build of the game with the costume "exists somewhere", but the costume was never made publicly available.

If the game is forced to select a language other than English or French, an unused flag of Spain will be shown in the Options menu. However, no script exists for the Spanish language, so selecting it will do nothing.

A prototype version of the game was distributed on some pirated cartridges featuring stickers for the game Daffy Duck: The Marvin Missions. The level select screen uses an unused rendition of "Hooray for Hollywood", while the Game Over screen uses the "That's All Folks!" theme. This is unlike the final version, which instead reuses the introduction and main menu music respectively. Other differences include the language selection screen being absent, and lives counting from 0 instead of 1.

According to each game's original director Taisuke Kanasaki, D from Another Code: Two Memories, and Will White from Last Window: The Secret of Cape West, are both intended to share the same birthday as him.

Ports of Donkey Kong 3 were developed by Hudson Soft for Japanese personal computers such as the NEC PC-8801 and Sharp X1 in 1984. These versions of the game were different in that Stanley is unable to jump, protecting plants is removed from the game, and most notably, the game's levels tell an ambiguous but bizarre story. The level backgrounds display a vastly different setting from the original arcade version, having Donkey Kong and Stanley traveling down a highway, encountering aliens, going to outer space, and landing on an alien planet. In the NEC PC-8801 version's manual, Hudson Soft encouraged players to develop their own explanation of the game's story and share it with them via mail.

In addition to the console versions, a Nintendo DS version of Crash Landed was being developed by Renegade Kid, which was known for their polygonal 3D games on the handheld. In 2013, Nintendo World Report released a 3-minute video of a playable demo for the DS version. The game was a 3D platformer, much like Renegade Kid's other cancelled DS project Maximillian and the Rise of the Mutant Mudds.

In an early version of the game, a pie weapon was planned to be included that allowed Bubsy to throw pies at enemies. However, this weapon would ultimately only appear in the Game Boy version.

When the game was first announced, it was referred to as "Code Name: X", with the only hint towards its connection to the Persona series being that it was claimed to be the first mobile game in a "famous Japanese console game series" that had sold over ten million copies worldwide. While the game's aesthetics and music were both noted to be reminiscent of Persona 5, and the file names for the game's artwork on the website were referred to as "P5", an official connection to the series was not discovered until the binary code at the end of the game's reveal trailer was translated to "Persona 5X".