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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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 Japanese version, before the fight against Captain Barbossa and the Illuminator in "Isla de Muerta, Port Royal" (1st visit), a cutscene plays of Jack Sparrow impaled by Captain Barbossa's sword off-screen, unlike in the film "Pirates of the Carribean: The Curse of the Black Pearl" in which it is shown on-screen. In the International release however, the sword was removed entirely.

In the Japanese version there's a cutscene which shows Donald Duck getting spanked by Daisy. This scene was changed in the International version to have Donald getting scolded instead.

In the Japanese release, after fighting the undead pirates during the first visit on The Interceptor in Port Royal, there's a cutscene in which Will Turner positions a pistol up to his head, as he does in the film "Pirates of the Carribean: The Curse of the Black Pearl". This scene was changed in the international release to have Will point his gun to the ground instead.

Yen Sid spoke for the first time in an episode of the "Wonderful World of Disney" (1971) called "Disney On Parade", in which he was voiced by Michael Rye. At the time his name was unknown, and he was referred to as "Merlin" by mistake. But his name was corrected when Kingdom Hearts II came out, almost 35 years later. He is voiced by Corey Burton, who still does Yen Sid's voice in other Disney animations.

Yen Sid's name is simply "Disney" backwards, and is supposed to represent Walt Disney himself.

Roxas has unused quotes in the game that can be activated when Spoiler:Guiding Minnie to the Hall of the Corner Stone so Sora, Donald, and Goofy can fix it. This suggests that Roxas may have once served a bigger playing role, or it was simply used for testing.

Despite Kanga's voice actress at the time, Kath Soucie, being a part of the game's cast, she surprisingly did not voice Kanga in the game.
Instead she was cast as Sally and Shock of the Halloween town world.

The voice actress for Vivi Orunitia, Melissa Disney, is a distant relative to Walt Disney. They are fourth cousins.

The title card for Halloween town contains an altered version of Kefka's laugh from Final Fantasy VI. The original Kingdom Hearts also has this, although its faster and harder to notice.