When Michael falls behind Peter, Wendy, and John as they are flying to Neverland, Michael sees Nana barking and uses Tinkerbell to sprinkle pixie dust on her. In the next shot as Michael flies away, John is right in front of him. This is impossible since the others were so far ahead of him, by this time they wouldn't be visible in the shot.
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 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.
Captain Hook is dueling Peter Pan in the scene with Tiger Lily. Hook almost falls when he steps off the ledge and his sword falls. In the next scene, Hook's sword is back in its scabbard as he hangs by his hook from a cliff.
The opening shot of the Darling house shows that the second story window to the parents' room opens out and the nursery window on the uppermost story closed. But once inside, the nursery has been opened - inward.
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.
When Captain Hook is confronting the Crocodile in Skull Rock, the Crocodile bites off a boot from Captain Hook's foot, However, before the end of the scene, the leg with boot and the leg without boot changes positions. When Captain Hook gets in the Crocodile's mouth for the last time, the boot is back on his foot again.
During the "Your Mother and Mine" sequence, some of the lost boys have war paint on their faces. They didn't have any on before Wendy started to sing. However, there's one shot during the fighting where the Twins have face paint showing on their faces.
When Peter Pan cuts the rigging, all the pirates fall into the lifeboat with Smee. There are about nine pirates falling into the boat, but when the fleeing Captain Hook passes them a few shots later, Smee has only four companions rowing the boat.
The pillow on a bench just inside the nursery window is round, save for a later shot, in which case, it is square. Likewise, the chair to the window's right normally has a red seat, but it turns blue temporarily.
One of the mermaids' hair color in the mermaid lagoon keeps changing. The one with upturned clam shells has black hair when she's first seen. Then a minute later it changes to blonde and another minute later it is red.
When Wendy and the boys are being put to bed, the covers on Wendy's bed aren't tucked in. Then when Peter Pan is looking into the window of the nursery, the covers on Wendy's bed are tucked in. Then after she wakes up, the covers are untucked and tucked in between shots. And in the last shot of her bed, the covers are tucked in.
When Captain Hook gets kicked on his head by a paddle from Smee and falls in the water with the Crocodile, the hook changes positions when Captain Hook swims up to jump on the boat with Smee. The hook normally has to be on the left hand.
When Mrs. Darling takes off John's glasses, she puts them to the left of his bed. Later, when Michael wakes John up and John says "Huh?" while putting his glasses on, he moves as if he took them from the right side.
When John is in bed, Mrs. Darling takes off his glasses and places them on a stand to the left of his bed. But when John wakes up later and puts his glasses on, he puts them on as if he's taking them from the right side of his bed.
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.
The goof items below may give away important plot points.
The redskins tie the children to a totem pole, to "burn them at the stake" - except that they'd never do this since totems are sacred objects bearing symbols of spirit beings and deities, as a reminder of the tribe's ancestry.
As the children wade through the straw-colored grass, they each leave a trail of crushed plants behind them. What appears to be a large gray rock turns out to be a huge rhinoceros - surrounded by undamaged grass as though the beast has never moved.