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 John and Michael are first learning to fly, they leap out of bed, throwing the covers back. When John leaps of the bed a minute later, both beds are perfectly made.
When the Lost Boys first come upon Wendy, Toodles is well behind the others. But in the next shot when Peter arrives, all the boys are together next to Wendy's body.
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 covers Wendy's mouth telling her to never say "I don't believe in fairies" the amount of dirt on Peter's hand repeatedly changes between shots.
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.
Before he goes ashore to capture the lost boys, Capt. Hook selects a double-bladed hook with the assistance of Smee. During the fight, he is wearing a standard hook with a single blade. In fact, after returning to the ship he is inside his cabin, emerging when the storm comes. During this time he could have easily changed hooks.
When John first learns to fly, the rigging holding him up is visible.
When Smee enters Hook's room and puts the clock in the table you can see bright markings on the floor indicating where the actor is supposed to walk.
Flipped shot. In the final duel between Hook and Peter in the air, Hook strikes Peter but his hook is on his left hand instead of his usual right.
Flipped shot in the nursery when Peter is standing at the foot of Wendy's bed. The strap of his outfit changes from his left shoulder to his right shoulder and then back again.
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!
When Wendy first enters the home beneath the ground, the boy who tumbles in from the left (the one Peter jumps over) is wearing white, high-top sneakers.