In the Japanese version, when you're done fighting the Nobodies with Axel to get to "The World That Never Was" in "Twilight Town" (3rd visit), there's a cutscene of Axel performing his special move which he looks like he's on fire and after he's done, there's a bit of fire around him. This was removed on all International versions of the game.

In the original Kingdom Hearts II on PlayStation 2, Kairi's underwear can be seen by maneuvering the game's camera angle. This was removed in the HD version.

In the game there is leftover code for some of Sora's animations he used in Kingdom Hearts. This includes stances, walking, attacking and jumping.

Found within the game's data is what appears to be a song based on "Eye Catching" from Final Fantasy IX, which is suggested to have played when Sora meets Vivi.

Spoiler:When Riku removes his bandana, the model continues to wear the bandana despite it also being in his hands until the next camera change.

There is an unused version of the song Lazy Afternoons that's more orchestrated. This is likely an earlier version of the song.

If the player has themed Command Menus turned on, "Hidden Mickeys" (a recurring symbol of the shape of Mickey Mouse's head inserted in plenty of Disney releases, theme parks and iconography) of varying levels of obscurity can be spotted in many of the area-specific menus. Some notable examples include:
• The gold gladiators on the Olympus Coliseum world's menu hold shields shaped liked Mickey's head
• In the middle of one of the gears in Hallow Bastion's Menu is a Mickey head
• The hard-to-see puffs of smoke "rising" out of the Underworld's Menu are translucent, wavy Mickey heads.

In areas where non-playable party members are walking around independent of Sora (i.e. the Bamboo Grove for instance), if the player looks at both Donald and Goofy from a distance they will sometimes walk toward each other and have a silent conversation. If Sora gets closer and approaches them, then they stop and focus their attention on him instead.

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.

Spoiler:Armored Xemnas' throne area visited during the final battle contains the signature weapons of some of the Organization XIII members that Sora had slain throughout the game scattered around the room, including: Xaldin's Spears, Saix's Claymores, Luxord's cards, and Demyx's sitar.

In a Kingdom Hearts Ultimania for this game, there was an early design for Roxas that was shown off where he had hair and attire that greatly resembles Sora's. Spoiler:One possible reason for the change was to better hide the fact that Roxas is Sora's Nobody.

Twilight Town had a radically different design in early concepts that featured a more fantasy-like setting with a fairy-tale-forest look that was complete with swampy ponds, grasslands, a train system that runs on large vines, and settlements atop incredibly large mushrooms.

There is a rare Reaction Command that can only be seen on the first ever visit to Hollow Bastion. In the event battle where Sora and Leon must destroy a posse of determined Nobodies in the Bailey and prevent them from breaking through the gates to the castle and town, in the rare occurrence that Leon manages to get knocked out, Sora can use a Reaction Command called "Recovery Run" to revive Leon while also spinning and attacking around him.