There are unused graphics of an "OK" button inside of the game's memory. It's purpose is unknown since menus in the game never ask you to confirm an action.
The games files contain an unused font, it's not known where it was intended to be used.
Sora's "Dive to the Heart" was intended to reappear in the game, but was removed during development for unknown reasons.
Marluxia was once planned to be another female organization member. This idea was scraped since the idea of the only two female members taking over a group of men might seem sexist. This made Larxene the only female, until Kingdom Hearts 358/2 Days.
Tetsuya Nomura has stated, in the Kingdom Hearts ULTIMANIA, that the game was originally called Kingdom Hearts Lost Memories.
Deep Jungle (The Tarzan World) was not in the game and it's remake "RE:Chain of Memories". The reason for the removal was that Disney and Square could not get the rights to use the concept and character from the copyright holders (the estate of Edgar Rice Burroughs).