When Peter knocks off Hook's hat and wig then they lands on the head of a Lost Boy, in the close-ups Hook's hat on the Lost Boy is crooked but in the shots of Peter and Hook where this boy is visible behind them the hat is completely straight.
When Peter is in the playroom at Granny Wendy's house, there is a teddy bear in the room. It's the same teddy bear that is found later by Peter in Neverland inside the tree but no-one brings the teddy back to Neverland when Peter goes there to save his children.
In the food fight the food covering Peter and the Lost Boys changes between shots. For example when Rufio throws the coconut the food on everyone immediately looks much dryer than before, and some of them have clean patches around their eyes that weren't there seconds earlier, these are both very noticeable on Peter.
When Tinkerbell starts glowing as she's turning human size inside the clock, the little curtains are fully open and you can't see Peter's hands; it then cuts to a shot behind Peter, his hands are suddenly now on the edge of the little window and the curtains are now more closed.
When the Lost Boys fire sticky arrows at Peter, at first there is no bright colored goo/paint on his clothes this doesn't appear until it changes to the next shot where Peter says "I've been shot" and he pulls and arrow off his groin.
When the lost boys are painting Peter for his first trial of flight in the sling shot the colors/design changes from when they paint him to when he is sitting in the sling shot. Most noticeably the white line on his stomach turns into a red happy face.
At the baseball game, Hook tells Smee to make the pirates switch HOME and RUN, he is seen yelling "Switch!" and then the scene moves to Smee standing at the pitcher's mound with a shocked look on his face and standing still as if he's been standing there for a while.
When the children are hanging in the net and Peter is trying to reach them, in the shot where Maggie says "Come on Daddie, Mommie could do it," she has both arms reaching out and Jack only his right arm. But as the next shot, from above, starts only Maggie's right arm and Jack's left are seen reaching out.
In the first shot of Hook's ship, panning down from the sails to reveal the bow with a skeleton on it, the catwalks and film lights in the upper reaches of the sound stage are visible above and behind the ship.
In J.M. Barrie's novel, "Peter and Wendy" (The original Peter Pan Story), Peter states that he cut off Hook's right hand, forcing him to fight lefty. However, in this film, Hook is missing his left hand.
After the dedication, Peter, Moira and Wendy approach the house and notice the broken glass at the front door (indicating someone has broken in). As they ascend the steps, there are slashes in the wallpaper as if Captain Hook has scraped his hook along the walls as he went up to capture the children. Captain Hook's hook is on his left hand, not his right. It wouldn't make sense for him to have done this on his way out, after having captured the children (plus, the slashes were made in an upward motion).
When Peter talks to Tinkerbell through the window of the clock house he puts his face right into the window. The outside shots show some kind of balcony/shelf outside the window, making it impossible for him to stand this close; especially when he puts his finger in his mouth like a thermometer as his arm comes from below, through where this shelf would be.
When Tinkerbell first encounters adult Peter in Wendy's home, Tinkerbell pulls a rug out from under Peter's feet, causing him to fall on his back. However Peter's feet leave the rug (the actor prematurely jumping) before it is pulled from beneath him.
As Peter attempts a front flip over the wall on returning home, when placing his hands on the snow covered wall top the whole row of snow moves slightly like a stiff solid, and his hands do not go into the thick snow even though he pushes down on it to jump.
The goof item below may give away important plot points.
In the scene when Hook tries to shoot himself, the pistol fires when the two men struggle for it and the shot sets on fire and sinks the toy pirate ship in the scale model of Neverland (a sinister omen of things to come). As the toy ship sinks, the pole/stand used to drag it underwater can be seen.