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 Dissidia 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.

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.

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.

In the secret ending of Kingdom Hearts II, Ventus, Terra and Aqua had capes on their armors. However, this was removed in Birth By Sleep due to frame rate issues.

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.

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".

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.

According to Tetsuya Nomura, 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:

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.

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.

In "Castle of Dreams", inside of Cinderella's house, it's possible to see "The Enchanted Rose" from Beauty and the Beast.

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, two Kairis can be seen. This mistake was fixed in Kingdom Hearts HD 2.5 Remix.

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.

There is an unused high poly version of the character Aqua present in the game files.

In Neverland, there's an unused room that only has a skybox of the night sky.

Outside Merlin's House in Traverse Town in the first Kingdom Hearts game, the likeness of an owl can be found on the broken archway in front of the house as well as in the form of several small statues surrounding the building. Outside Merlin's House in Hollow Bastion/Radiant Garden in subsequent games, this owl's presence is reduced to two emblems hanging over Merlin's front door both inside and outside the house. These owls are a reference to Merlin's pet owl Archimedes, a character from Disney's 1963 adaptation of "The Sword in the Stone", who does not appear in the Kingdom Hearts series.