In the Japanese version version of the game, it's only possible to earn Mission Crowns by playing the game's Mission Mode in multiplayer, but in the western versions, the player can be awarded crowns in both single player and multiplayer modes.

In the western versions of the game, the mission mode difficulty was toned down. As a result of that, enemies are given less HP, the player is awarded Munny for beating missions, and some of the enemies enemies take less damage than they do in the Japanese version.

Xion seems to have been named after the Shion flower (more commonly know as Aster Tataricus). In Hanakotoba (Japanese flower language), Shion is used to convey "memory" or "to remember someone." Spoiler:This could be a reference to her being made out of Sora's memories and/or a cruel irony on the fact that nobody remembers her by the end of the game.

Tinker Bell was made mute, so she doesn't have spoken lines in this game. Hence, her face sprites went unused as well.

When entering Wonderland for the first time, a scene showing Sora fighting several Possessors will play out. This did not appear in the first game.

358/2 Days is the last Kingdom Hearts game and Disney product voiced by Wayne Allwine, Mickey Mouse's third voice actor, before his death. The game is dedicated in his honor in the English version.

Near the end of the game, Spoiler:Roxas has to fight Xion, who wants to absorb him. During the 3rd phase of the battle, Xion transforms into a form that looks a lot like Kurt Zisa. This makes sense since Xion is using Sora's memories as a weapon and they are fighting in Agrabah, where Sora previously fought Kurt Zisa in the first Kingdom Hearts.

It was originally planned for Pinocchio's world to be a location in the game, but it was later removed due to space limitations. Mugshots for Pinocchio as a human, Gepetto, and the villains Honest John and Gideon are left in the game, unused.

Hades and Megara were planned to appear in the game. Profile sprites were made for the characters that can still be seen in the game data by hacking the game.