When Hook gets the idea to manipulate Tinker Bell, he calls for Smee to give him his best hook. Hook then takes a golden hook and replaces his normal silver one with it, screwing it into the silver base. However, in the next scene, after throwing Smee from the room, the base is inexplicably gold. It remains gold in the scene with Hook and Tinker Bell. Also, Hook previously placed a ring on his golden hook and it is not present during his scene with Tinker Bell.
After Mr. Smee gives Hook a shave, they see Peter Pan and the Darling children arriving at Neverland. Hook calls for Smee to raise the crew which he does with a whistle hanging around his neck - a whistle that wasn't there until that moment.
When the children are in the nursery being tucked into bed, Wendy's pillow changes from being striped to being white and then striped again.
In the "Indians in the trees" scene, Michael's pajamas change from original pink to white and then back to pink.
When Hook sits down in a chair for his shave, he is well away from the side of the ship. But in the next shot, he leans back in his chair against the side of the ship. After the Crocodile arrives, Hook bolts from the chair into Smee's arms and the camera pans from the chair he was sitting on over to a second chair on the right. No second chair is seen before then.
When Peter Pan rescues Tiger Lily and he is flying her away, she spits out water and her lips move to say "thank you" but no words come out. This is a common occurrence when one's breathing has been impaired.
Shortly after Wendy leaves Big Ben's hands, her face disappears. All that is showing is a blank pink area (play the DVD in slow-motion).
When Hook, Tink, and Smee are all in Hook's cabin and he goes to drag a drunken Smee out, he is dragging Smee with the hook surprisingly on his right arm.
As Peter, Wendy, John, Michael, and Tinker Bell near Neverland (toward the end of the "You Can Fly" sequence), Peter's shoes change from brown to green.
During the song "The Elegant Captain Hook", Wendy's hair color changes several times. Additionally in the same scene, there are shots where Wendy is not present at all.
When Wendy is being splashed by the mermaids and she says "If you dare to come near me again..." her mouth isn't moving.
Smee tells Hook that the cook told him that the first mate told him that he heard that Pan had banished Tinkerbell but technically Smee is the first mate.