Jane steals the key for Peter's bonds from Hook. During the following chase up and down the ship ending with Jane flying around and finally landing near Peter to free him, the key is in her left hand, gone, in her right hand, gone, in her left hand, gone and finally in her right hand.
Jane falls into the ground leaving a Jane shaped hole. When she climbs out the hole is a slightly different shape. And later the Jane shaped hole is suddenly gone.
When Hook is getting a massage by Smee, and is surprised by the Octopus, when Smee is getting rid of the Octopus, he is standing on the right side of the Ship, but when Smee gets water in his mouth by the Octopus, the place where he stands changes from direction.
Wendy's husband leaves to fight in WWII as the Battle of Britain is beginning. This occurred in 1940, prior to US active participation in the war, but the military truck he leaves home in has the "circled star" roundel of the United States Army rather than the "bullseye" roundel of the UK or the "crowned lion" logo of the British Army. While he has a British army type cap but American sheepskin type jacket and trousers tucked into American long boots.
In one scene when the Lost Boys mentioned about "faith, trust and pixie dust", Nibs had Slightly's voice and vice-versa.
During the opening sequence, the camera show river Thames, with the Tower bridge and the Big Ben clock tower very near to each other and only one bridge in the middle. In fact, both landmarks or not even close to each other and it is impossible to see them in the same frame, due to the shape of the river. Besides, there are many bridges in the middle - Westminster, Charing Cross, Blackfriars, the London Bridge and others - as well as St. Paul's Cathedral. Neither of them are shown in the sequence.
Midway through the film, Hook sends his crew ashore in search of Peter and the Lost Boys' hideout, with Smee complaining about the number of times they've combed the island looking for it. But Peter's hideout appears to be the same one Hook learned the location of in the first movie - why does he need to go looking for it again?
The voice of Cubby (the Lost Boy in the bear suit) is very different from the one he had in Peter Pan (1953). In the first film he had a deep "bumpkin" voice, in this one he speaks with a much higher pitch.
Many older viewers have questioned about grown Wendy, who's presumably in her early 50s, (as she was aged around 12 or 13 in the first film, and this one is set 40 years later) having a young boy who appears to be younger than five years-old. It's as if her biological clock lasted longer than the average (women giving birth in their late 40s was very rare back in the 1930s) or she adopted him herself.