While playing the Atlantica Rhythm mini-games in the Japanese version, the O button is used as a rhythm trigger a majority of the time. In the English version it's replaced with the X button.
In late March of 2007, Kingdom Hearts II: Final Mix+ (2007) was released in Japan, containing that disc and a remade-for-PS2 version of Kingdom Hearts: Chain of Memories. The Final Mix version contains many changes, including: Puzzle Mode, Theater Mode, fights with all 13 Organization members in a secret room, all-new cut-scenes, a new Drive Form, and other things.
Port Royal has many edits on the non-Japanese versions. Cut scenes were edited to remove some of the violence, such as Will Turner threatening to commit suicide while aiming a gun at his head. While he still threatens to commit suicide, he does not aim a gun at his head. In the original Japanese version, the blood on the cursed medallions remains throughout the game, but disappears after Barbossa and Will drop them into the chest. However, if one looks closely, blood is visible on the medallion while Sora is holding it. Also, when Jack Sparrow is stabbed by Barbossa, the sword sticks out of his chest as he staggers back into the moonlight. In the English version, the sword has been removed.
Further edits to the Port Royal world for non-Japanese versions of the game include the following: Barbossa's monologue to Elizabeth on the Black Pearl edited to omit the mention of lust and women; undead pirates not catching fire (though such is still the case for the Grim Reaper Heartless); and the Rifle Pirates' guns being replaced by crossbows (though they still sound and function like guns).