In Land of Dragons, after the Captain finds out Ping is really Mulan, he tells the rest of his troops "Move out!" He then leads the group away. However, after all the troops have passed by, you see the Captain following behind them at the back of the group.
Right before you play the "1,000 Heartless Challenge", there is a cut scene in which Mickey runs after Xemnas, leaving Sora, Goofy, and Donald behind. The trio is then surrounded by Heartless. There is a shot of Sora, who looks over his shoulder at Donald and Goofy. The shot then changes to Sora again, who runs to attack the Heartless. In these scenes, each character has their most basic weapons they start with in the beginning of the game.
In the ending when Sora is reading the letter from Kairi, they spell the word "starting" wrong. It is written "Now I will step forward to realize this wish. And who knows. stating a new journey may not be so hard."
When Luxord invokes the Pirate Code (the right of parlay) in Port Royal, Jack Sparrow accepts this. However, as stated in Pirates of the Caribbean: The Curse of the Black Pearl, one must be a pirate for the Code to apply. Sparrow should have known this of course, and ignored Luxord's request.
After the Heartless damage the Winnie the Pooh book, Sora enters the book again. Pooh starts his "stoutness exercises". He first touches his toes, then lifts his right foot. The angle changes, and you see him from the back. Pooh touches his toes, and lifts his right foot again. It is obvious from the next few exercises he does that he should be switching feet.
Ursula doesn't remember Sora, Donald and Goofy, although other resurrected characters (Jafar, Oogie Boogie, Maleficent) do. Maleficent, who returned in the exact same manner as Ursula (using the powers of darkness), does remember them, so there is no reason Ursula shouldn't.
Pete's journal entry in Pride Land claims he is 'aiding Scar's phantom'. However, Pete only appears during the first visit to Pride Land, whereas Scar's ghost doesn't appear until the second visit. Also, Scar's ghost is already mentioned before it appears (and before Scar is even defeated).
In the Aladdin cut-scene where Jafar has Jasmine chained to the door, Sora, Goofy and Donald appear with Aladdin. Sora, Donald and Goofy hold weapons and shields. However after Jafar zaps Iago with his staff, everyone runs over to him, and they are all now empty handed.
After the Organisation XIII scene, just before Sora takes out his member card, Goofy's shield just disappears from his hands. Many other times during cut-scenes, weapons and shields just vanish from hands as well.
Right before the fight with Barbossa, Barbossa stabs Jack Sparrow off-screen, exclaiming he's a fool. He raises his hand, his sword gone. However, when Jack staggers backwards, there is no sword in his chest.
When Roxas sees Sora's memories in his dreams, he also sees scenes that Sora never witnessed, such as Jafar's line "The boy is a problem; he found one of the Keyholes" which was at Maleficent's council in Hollow Bastion. Sora was never present to hear Jafar say this line.
Scrooge McDuck's journal entry states that, 'Before the Heartless appeared, he was using the Gummi Ship to travel across worlds'. However, in the first Kingdom Hearts it is stated that, before the Heartless came, 'impassable walls' divided the worlds, making inter-world travel impossible. It only became possible after the emergence of the Heartless, who destroyed the walls.
In Port Royal, to end the curse of the Aztec gold everyone who has touched the golf must pay in blood. However, when Jack Sparrow tosses the coin to Will he doesn't cut himself to pay in blood as he does in _Pirates of the Caribbean: The Curse of the Black Pearl (2003)_.
It is clearly stated in the first game that Sora, Donald and Goofy must not meddle in the affairs of other worlds. All their actions in the various worlds they visit are to stop the Heartless and other foreign villains from meddling. However, in Atlantica, which is free from Heartless and also not visited by Pete or Maleficent, they have no problems interfering to help Ariel against Ursula.