Continuity mistake: When we see the windows of the Darling nursery, at the start and at the end, their height repeatedly switches between having either five or six horizontal rows of glass panes.
Audio problem: After the mermaids splash Wendy, she raises a seashell threateningly above her head and says "If you dare come near me again.". Her mouth doesn't move at all.

Continuity mistake: In the scene where the crocodile attacks Hook at Skull Rock, there is a shot where the croc bites Hook's left foot and the shoe comes off, leaving Hook's left foot bare. In the shot with Hook wrapped around the croc's snout, the shoe is back on Hook's left foot and his right foot is bare.
Continuity mistake: After Peter cuts the rope around the mast where the kids are tied, there's a brief shot of Peter standing sideways on the mast. Look below and you'll notice that the ropes have vanished.
Continuity mistake: At Hangman's tree, while the Lost Boys dance, Wendy grabs Michael's feather and tomahawk and lays them on the floor. A shot later they're nowhere to be seen.
Continuity mistake: After Tinker steps on Hook's map and draws an X where Peter is, the X and the ink spots on the paper disappear.
Continuity mistake: When Mrs. Darling is about to leave and Wendy is dozing, her pillow swaps from being opened and striped inside, to fully closed and totally white.
Continuity mistake: When Hook sits down to get a shave his chair is a couple meters away from the side of the ship. A shot later it's centimeters away.

Continuity mistake: The first time we see the pirates a group of them are doing dagger-throwing at a chalk drawing, but in the very first shot the drawing is missing.
Deliberate mistake: During the first aerial angle of the pirate ship they are heard singing, but the ship is empty. Most surely due to the complexity of drawing detailed tiny pirates.
Continuity mistake: When the bomb explodes, Wendy and the kids disappear from the side of the ship, only to reappear in the close-up.
Continuity mistake: The seashell that Wendy uses to defend herself from the mermaids magically appears after several shots.
Audio problem: When the mermaids are nagging Wendy they cry "Oh please!" "I insist!" but their mouths aren't moving.
Continuity mistake: When Michael checks who's underneath the moving tree, the tomahawk on the ground disappears between shots.
Continuity mistake: After Michael grabs the tomahawk stuck on a tree he walks to an area with grass. In the close-up he is standing on sand.
Continuity mistake: When John and the kids walk by the Native American area, in the aerial angle the Native American's footprints disappear.
Continuity mistake: When we see Tiger Lily tied up to the anchor, the left side of the rope goes over the right side. A shot later it's the other way around.
Continuity mistake: When the movie ends, Mr. And Mrs. Darling, Wendy and Nana are by the window looking at the sky. In the aerial angle they all disappear.
Continuity mistake: When the ship turns to gold and starts to fly everyone disappears.
Continuity mistake: After Hook swims away, Wendy asks Peter where are they going to. The rope behind her swaps positions between shots.
Chosen answer: He's too much of a bumbler and too cheery (for example when he tells the crew "good morning" and they wanted to know why it's so good.) They probably also see him as a fool and brown-noser since he's always trying to make Hook happy. To the crew he's just Hook's assistant and not a real pirate at heart.
Bishop73