Videos
Kingdom Hearts - Did You Know Gaming? Feat. Yuriofwind
 
In Neverland, there's an unused room that only has a skybox of the night sky.
Contributed by CuriousUserX90
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There is an unused high poly version of the character Aqua present in the game files.
Contributed by billebobfacts
The game has an updated version of the song "Dive Into the Heart" from the first Kingdom Hearts game using the Birth by Sleep instrument set, which goes unused.
Contributed by CuriousUserX90
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In the cutscene where Aqua meets Kairi and King Mickey for the first time. If one pauses it at the right moment and looks closely they can see 2 Kairis. This mistake was fixed in Kingdom Hearts HD 2.5 Remix
Contributed by billebobfacts
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In "Castle of Dreams", inside of Cinderella's house, it's possible to see "The Enchanted Rose" from Beauty and the Beast.
Contributed by ProtoSnake
The director of Birth by Sleep, Tetsuya Nomura, specifically requested that Master Eraqus would be voiced by Mark Hamill, known for his role as Luke Skywalker in Star Wars. He also requested that Master Xehanort be voiced by Leonard Nimoy, known for his role as Mr. Spock in Star Trek.
Contributed by Badsauser
Zack is the only Final Fantasy character to appear in the game. Other Final Fantasy characters were originally planned to appear but Tetsuya Nomura thought that they would have made the story go too far off track.

Zack was chosen to be the only Final Fantasy character due to the fact the development team wanted a character that was from the past to fit with the prequel story.
Contributed by gamemaster1991
Vanitas' name is derived from the Latin word for "Vanity" or "Emptiness". The name was chosen for its meaning, the similarity to the name "Ventus", and as it's a written pun on "Sora" in Japanese.

Tetsuya Nomura: I wanted to give him a name that meant "empty", and so I looked for something that would be appropriate. When I was searching I found a word that meant "emptiness" in Latin, "Vanitas". It looked a lot like Ventus's name, and in Japanese it has the kanji for "sora" in it, so I thought it was perfect. Of course in Vanitas's case it doesn't mean "sora [sky]" but "kara [empty]" [These two words are written with the same kanji, but are said differently and have different meanings.]
Contributed by Tuli0hWut
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Master Eraqus physically resembles Hironobu Sakaguchi, the creator of the Final Fantasy series. His name is also an anagram of "Square", a reference to Square Enix, the developers of the Kingdom Hearts series.
Contributed by Pogue-Mahone
Some unused 3D models and an image of the demo of Kingdom Hearts 3DS: Dream Drop Distance's logo can be found in the Japan-only Final Mix re-release, hinting that KH 3DS: DDD uses a modified Birth By Sleep graphical engine.
Contributed by WhiteSamurott
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Through the use of cheating devices in the Japanese version of the game, the player can obtain a version of the Kingdom Key D called "Light Seeker".
Contributed by SiiGMA Viperz
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In Deep Space, Pleakley from the Lilo and Stitch film was originally going to be present. He was removed for unknown reasons, but a character model can still be found in the game's code.
Contributed by SiiGMA Viperz
In the secret ending of Kingdom Hearts 2, Ventus, Terra and Aqua had capes on their armors. However, this was removed in Birth By Sleep due to frame rate issues.
Contributed by Shinitenshi
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Aqua's design was somewhat different in early development. Her back was more exposed in the beginning but in the final version was more covered. There was also a point when her hair and eyes were darker, and lacked the sheen of the final game.
Contributed by Shinitenshi
There was a world based on the Jungle Book made for the game, but was removed for unknown reasons. The world can still be found in the code and can be accessed using a cheat device, though it's unfinished.
Contributed by gamemaster1991
Laguna, from Final Fantasy VIII, was planned to be included in the game as head of the Mirage Arena but Square Enix was also planning for him to be in Dissida 012 Final Fantasy which was being developed around the same time. Developer Nomura Takahashi decided that they wanted Laguna to be in Dissidia more and made the decision to leave him out of Birth by Sleep.
Contributed by Shinitenshi