In the Proof of Existence area of the Castle That Never Was, there are panels for each of the Organization members, represented by that member's weapon. However, Zexion's panel is so damaged, it's impossible to see his weapon. This is due to his weapon not being revealed in Kingdom Hearts: Chain of Memories, as the player never fought him.

Cloud's appearance in Kingdom Hearts II was based off of his appearance in Final Fantasy VII: Advent Children.

Members of Organization XIII were supposed to be enemies in Olympus Coliseum battles, but were left out of the original game's release due to time constraints. They were later included in the Final Mix version of the game.

According to series creator Tetsuya Nomura, the idea to put sea salt ice cream in the game came from when he was invited to the opening day of the theme park Tokyo DisneySea in 2001, where they sold this type of ice cream. He stated he liked the treat so much that his image of Disney strongly overlapped with it. He asked Disney if he could put the ice cream flavor into the game as a treat the kids in Twilight Town ate during summer vacation, but clarified that the game's writer Kazushige Nojima was responsible for incorporating this detail so heavily into the game.

Through the use of a cheating device, 2 alternate versions of the Ultima Weapon can be found. These weapons are titled "Edge of Ultima" and "Detection Saber". In game they are given a glitched appearance and are only palette swaps of the original Ultima Weapon. They are also missing a menu picture, and instead a map is displayed.

According to the trailer, the castle at Hollow Bastion from the first game may have been where Sora first met Organization XIII, instead of in the bailey like in the final version.

The Fenrir Keyblade's appearance in Kingdom Hearts II is based on a pin tumbler lock key unlike all other Keyblades. The name comes from Norse mythology and is also a reference to Cloud's motorcycle in Final Fantasy VII Advent Children.

The character Chicken Little from the 2005 film of the same name was the first computer-generated Disney character to appear in the series. The character was included as a summon to promote the film's theatrical release in Japan on December 23, 2005, one day after Kingdom Hearts II's Japanese release.

Xigbar's weapon was changed for the American release. In the Japanese version, he carried a weapon that resembled a sniper rifle and his scope included a cross-hair while zoomed in. In the American release, his weapon was changed to look less like an actual rifle. His weapon was split into two blades, and his scope was changed to include a three circles design instead of a cross-hair. This is one example of many changes from the Japanese version.

In a beta picture of "The Battle of the 1000" at Hollow Bastion, there appears to be two Behemoths standing in the middle of the Heartless army with Sora, Donald and Goofy charging at them. This would imply that you would fight more types of Heartless than the Armored Knights and Surveillance Robots. Also that Donald and Goofy would be a part of the battle. According an interview with the director, Tetsuya Nomura, the battle was so big that the team almost dropped it from the game even without the extra Heartless, due to the sheer quantity of enemies on screen.

Gaston's absence from Beast's Castle (the "Beauty and the Beast" world) makes him the first Disney villain to not appear in the Kingdom Hearts series with a world based on his movie featured as a playable level.

Originally, the final boss, Xemnas, was going to have another final form.

Selphie incorrectly refers to Tidus as "Tie-Dus" instead of the correct pronunciation of "Tee-dus" during a cutscene with Kairi.