Continuity mistake: When Smee and Captain Hook are alone on the ship at night, Smee stands up just after eating chicken off his plate. His blue bandana hangs down his left shoulder near his plate. However, after a shot of Hook when it faces Smee again his bandana is now short, just resting on his left shoulder.
Continuity mistake: After finding his son hit a home run in the game with the pirates, Peter decides he must learn how to fly. The ball his son hit comes flying from the sky and hits Peter in the head, knocking him over. When he hits the ground, he is lying on grass, but one second later he opens his eyes on grey rock.
Continuity mistake: When Smee gives Hook his nightcap drink, Hook takes it in his hand and holds it at the top of the goblet so that it is hidden under his hand. But in the very next shot he is holding it by the handle and the whole goblet is now visible with a small black umbrella sticking out the top. Additionally, the position of the small umbrella that sits in the goblet changes a few times.
Revealing mistake: In the last scene that we see Maggie and Jack before they are kidnapped, when the bed covers fly off their beds, you can see that they are suspended by their corners. This is particularly obvious when they are lifted up. The middle of the quilt sags while the corners are lifted.
Continuity mistake: When Peter is fighting Hook in front of the crocodile clock, he uses his sword tip to fling the pirate-hat and its wig attachment off of Hook's head and it flies over and lands on one of the Lost Boys heads. When it lands on his head it is wonky. But in the next shot it is sitting on his head perfectly straight and is then wonky again in the next shot.