According to Chris Glass, a member of the game's development team, the texture used for the bark on tree trunks is simply a green-tinted photograph of feces.

Bubble Bass has unused eye textures in the GameCube, PlayStation 2, and Xbox version's files, suggesting he may have been planned to have a larger role in the game.

The "Under Siege" musical theme appears to be based on part of Gustav Holst's "Mars, the Bringer of War" suite from Opus no. 32 "The Planets", this is appropriate due to the heavy war theme of the game and the situation the characters are in when the theme plays.

On the NES verion's System Construction Figure menu, inserting certain inputs will cause the cursor woman to remove her clothing. The final input freezes the game and replaces the woman with a hexagram.

The Arcana Edition of the game, which will be released for the Nintendo Switch and PlayStation 4 exclusively in Japan, comes packaged with exchangeable sleeves and a set of tarot cards featuring various fighters from the series.

If you enter "REFLOG" as a player name in the Genesis version, you will be brought to a secret golf mini-game.

Unused text in the GBA version's files suggest that all of the in-game spells (except for Expelliarmus) were planned to be upgradeable.

Fully modeled, unused traffic cars can be found in the game's data. They include an ambulance, a camper, and two trucks (one with a truck hauling pipes, and a tanker truck).

The Wart Boss Fight was originally going to sport tomato projectiles like its original incarnation in Super Mario Bros 2 featured. They were replaced with cabbages in the final release, but the tomato sprite is still present in the game, albeit unused.

The Gamecube version's code has unused text lyrics from Bob Gibson's song "To Morrow."

The texts states:

"If you had gone to Morrow yesterday, now don't you see
You could have gone to Morrow and returned today at three!"

The Korok seeds Link finds are actually Korok excrement.

Early music icons for the SpongeBob SquarePants DLC can be found in the PlayStation 3 version's data. They do not feature any LittleBigPlanet characters.

Entering the Konami Code on the title screen will change the game's logo from "Super Monkey Ball Jr." to the message "Super Nice Try".

The Xbox 360 version has text stating "PS3 Online Data Incorrect,". This suggests that a PlayStation 3 release may have been planned at one point during development.

In the Octo Expansion, the title for Stick 'n' Move Station is a reference to a line in the 1979 film Rocky II, where the character Tony Evers tells Apollo Creed to "Stick and move." The tagline is a reference to Muhammad Ali's famous line about his boxing style, that he would "...float like a butterfly, sting like a bee!"

Paper Luigi was originally intended to be playable as well, but he ended up being excluded, because the game became too complicated with his implementation.

In the Octo Expansion, the taglines for all the 8-Ball stations are possible answers for a Magic 8-Ball:
• "Signs point to yes..."
• "Better not tell you now..."
• "It is decidedly so..."
• "You may rely on it..."
• "Outlook not so good..."
• "Reply hazy, try again..."
• "As I see it, yes..."
• "My sources say no..."
• "Cannot predict now..."
• "Don't count on it..."

The South Korean exclusive version of the game is called Destiny: Guardians. All content in this version is the same as the international versions, with the exception of the microtransaction vendor, Tess Everis, being replaced by Yuna, an original character created exclusively for this version that offers different items.

Despite the fact that multiplayer-heavy games like Splatoon 2 required the use of a phone app for online voice chat previously, it was discovered in early June 2018, around the time of E3, that the Switch actually had the ability to have Native voice chat, a feature that was finally implement with the help of Epic Games. It can be accessed by plugging in a set of headphones with voice capabilities. Nintendo enabled this feature on June 14th with the first game utilizing it being the widely popular Fortnite.

It is unknown why this feature was previously unused.

The text used in the cutscenes of this game is a purple colour in the Japanese version, but white for the US and EU versions.