Deep Jungle (the world based on the 1999 film adaptation of the book series "Tarzan") was originally planned to appear in the game, appearing in an early prototype mock-up image of the card battle system. However, it did not appear in the final game and has not appeared in any new Kingdom Hearts titles outside of the first game, likely due to copyright issues between Disney and the estate of Tarzan creator Edgar Rice Burroughs.

Kingdom Hearts: Chain of Memories originally went under the tentative title of "Kingdom Hearts: Lost Memories". Series creator Tetsuya Nomura changed it to the final subtitle because he thought it "had more style and it matched the general outline of the story too (i.e. Sora relieving a succession of memories, a chain)".

According to character designer Tetsuya Nomura, Marluxia was originally planned to be another female Organization member. However, this idea was scrapped because they felt the idea of Marluxia and Larxene, the only two female members, betraying and taking over a group of men would seem unbalanced and sexist. This made Larxene the only female member of the Organization, until Kingdom Hearts 358/2 Days.

Sora's "Dive to the Heart" was intended to reappear in the game, but was removed during development for unknown reasons.

The games files contain an unused font, it's not known where it was intended to be used.

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.

There is a wrong volume event in the game that causes the song, The Force in You, to not play one of its channels. This mistake was fixed in the game's remake.