Continuity mistake: In the duel at Skull Rock, after Peter leads Captain Hook onto thin air, Hook drops his sword and scrambles to grab hold of the cliff again. But when we see Hook's reaction to the approaching crocodile, you can see his sword back in its sheath.
Continuity mistake: After the mermaids splash Wendy with a ton of water, her hair is wet and you can tell because it is sort of hanging down and drooping. Then they cut away, then when they cut back to Wendy, her hair is perfectly dry.
Continuity mistake: As Peter Pan flies up to get his hat back from Captain hook in Skull Rock, he stops in midair and has a shadow, and then the picture changes to Wendy, who then says, 'whew' and then it changes back to Peter and he doesn't have a shadow.