The names of the post-game master trainers appear to be references to other outside media:
•The Pikachu master trainer Lass Iuke is a reference to voice actress Ikue Otani who voices Pikachu in the Pokemon anime.
•The Eevee master trainer Lass Aoi is a reference to Aoi Yūki, the voice actress for Eevee in the game.
•The master trainers for Zubat and Golbat, Scientist West and Scientist Keaton, are references to actors Adam West and Michael Keaton, respectively, who both played the superhero Batman.
•The master bird trainers Bird Keeper Barney, Bird Keeper Seymour, and Bird Keeper Moe, are possible references to the characters Seymour Skinner, Barney Gumble and Moe Szyslak from the animated series The Simpsons.
•The three ghost master trainers: Psychic Arin, Psychic Danny and Psychic Ross, are references to the members of the video game web series Game Grumps; Arin Hanson, Danny Avidan and Ross O'Donovan.

A large area of the game, titled The Boneforest, was cut late in development.

The GameCube version contains Mario, Luigi, and Peach as playable characters. This was part of a deal EA made with Nintendo on using third-party characters for their games.

A physical release of the game had been planned and to be published in partnership with Skybound Games. However on November 10th, 2018, it was announced via the developer's blog that the release had been cancelled due to the process proving to take more work than had imagined, especially since the game's development team only consisted of three people.

In an interview with Junichi Masuda, he stated that the source data for the game was almost lost because the computer that stored the data suffered from a nasty crash.

Stacking 30 goombas is the normal limit in game, but it's possible to stack 200. Going over this amount crashes the game.

Ridley's orange pallet swap is in reference to the villain'a appearance on the box art of Super Metroid.

The license plate on Claire's motorcycle, "J2198", is a nod to Resident Evil 2's original release date, January 21st 1998.

The infamous Red LED lights that surround the 360's power button actually represent different problems depending on how many are alight. One red light meant a hardware failure. Two red lights signify overheating. Three red lights meant a general hardware failure, and four red lights meant and AV cable error. The notorious "Red Ring of Death" is actually, contrary to it's name, a 3-Light problem (General Hardware Failure).

According to Nintendo's Kensuke Tanabe, a horror game starring Tingle began development in 2010. It would've been developed by Vanpool, the developers of the Dillon series. Nothing else is known about the project, except that it was canceled due to "a variety of reasons".

According to a Famicon Tsuushin magazine interview, with Shigeru Miyamoto, the cars in the game hover so that Nintendo didn't have to animate the car's tires.

Found within the game's data are unused themes of the mini-games "Let's Get a Move on" and "Pandemonium" from Mario Party 3 and 9 respectively, suggesting mini-games from Mario Party 3 and 9 that used those tracks were intended to be included in the game.

In the publication "The Legend of Zelda Encyclopedia" by Dark Horse Comics, it was strongly suggested that the entirety of the first legend of Zelda game actually takes place on Death Mountain. Furthermore there are a lot of similarities between the entire map of The Legend of Zelda and the Death Mountain portion of the overworld from The Legend of Zelda: A Link to the Past, giving more credence to the claim.

38 Studios was founded by former Boston Red Sox all-star pitcher Curt Schilling with backing from the state of Rhode Island as a way to help the state's struggling economy. The company only released one game, Kingdoms of Amalur: Reckoning, which was regarded as a commercial failure and the reason behind the company going bankrupt.

There's unused longer versions of each dance jingle used in the game.

When the designs for the first 8 characters (Alice, Snow White, Red Riding Hood, Sleeping Beauty, Cinderella, Pinocchio, Gretel, and Kaguya) were revealed, the notes by the director and author, Yoko Taro, repeated "Very cute! I believe she’ll/he'll sell well!" for each character. When the 9th character (Little Mermaid) was revealed he used his note to directly address his lackluster comments:

"I’ve been commenting my honest feelings of “Very cute! I believe she’ll sell well!” about all the designs we’ve presented up until now, but someone pointed out that “Yoko Taro is really slacking it with his comments.” So this time, please allow me to change the comment to: “If we’re talking cute or not cute, then she’s very cute! If you’re wondering whether she’ll sell well or not sell well, I think she’ll sell well!! But even if she does sell well there won’t be any money in it for me or Jino-san, and I can’t sleep at night thinking about the wonderful people at Pokelabo or Square Enix pocketing the money!”

Alice has several pocket watches underneath her maid outfit. A detail that was revealed by the character designer, Jino, and cannot be discovered playing the game.

The Conner android has several possible references to the Terminator film franchise. Conner is an "RK800" model, just as Arnold Schwarzenegger's character from the films is a "T-800" model initially. The name of the robot from the game is "Conner" which is very similar to the surname of two central characters from the films: Sarah Connor and John Connor. The Trophy for letting Conner die every way possible is called "I'll Be Back" which comes from Schwarzenegger's icon line from the first Terminator film.

There are hidden rooms in the game's code. Some of the hidden rooms are part of cutscenes, while the rest are designed for boss fights. The only way to access hidden rooms is to hack the game's save files.

In an intro dialogue with Michelangelo and Atrocitus, after Atrocitus says that he "could wear a red ring", Michelangelo will reply back saying how he "should have worn the red bandana." A reference to how Michelangelo wore a red bandana in the original Mirage Comics.