When the pirates realize the "crocodile" is up in the rigging, Hook is holding Michael and then throws him down to the ground. When Hook re-emerges after getting weapons, it is John that's on the ground (whom he kicks), not Michael (who is still sitting with the lost boys).
When the crocodile appears at the Black Castle, a close-up of the boat shows Wendy leaning over the side closest to the crocodile, but on the next shot from Hook and Peter's view, she's sitting on the opposite side closest to the rock.
When Peter is leading Wendy to the window ledge he is shown with the curtain blowing in front of his face and being lit from the front but the only light is coming from inside the nursery and the curtains are blowing in. This indicated that he is outside of the room but the next instant he is beside Wendy inside the room. A nearly identical shot of Peter comes a few seconds later after he has been seen leaving the nursery and is floating outside of the window.
Before the final fight on-board his ship, Capt. Hook selects a double-bladed hook with the assistance of Smee. During the fight, it has obviously changed back to his more common standard hook with a single blade.
During the duel Peter reveals that Hook's first name is "James". The plaque on the door to his cabin states that it is "Jas." which is a common way to abbreviate the name "James" (not, as some believe, an abbreviation for "Jason Isaacs") and is actually lifted directly from the original story.
The shot of John skewering the bookshelf is flipped. John lunges with the sword in his left hand, but completes the motion with the sword in his "right" hand. The part in Wendy's hair changes sides as well!
The goof item below may give away important plot points.
Just before engaging his duel with Peter, Hook throws his large feathered hat overboard, and it is heard hitting the water. Later, when Hook is finally defeated, we see Peter wearing proudly the hat which is totally dry with no evidence that it had ever been "fished out" of the water.