Continuity mistake: When Harry goes back to Hogwarts and they stand before the Fat Lady portrait she refuses to let them in because she's trying to show them she can break a glass with her voice. When she cannot she smashes it upon a brick wall behind her right shoulder. Later in the movie after the students gather around the Fat Lady's painting after it's slashed the wall is missing.
Continuity mistake: When Harry is talking to Sirius (the first time), Hermione yells to Harry to get his attention about Lupin. In the background, you can see Hermione sitting next to Ron right as she starts to say "Harry." In the next shot, she is standing up farther away from Ron (this is visible in the widescreen DVD only).
Continuity mistake: In the shrieking shack, the cobweb on the ceiling changes position between shots.
Continuity mistake: When Harry is on the Knight Bus, Stan Shunpike has acne on his neck that keeps changing. Sometimes there is a whitehead, and other times it's just a red mark.
Continuity mistake: When Ron and Hermione are arguing about Crookshanks in the Leaky Cauldron, Sirius does not move in the 'wanted' poster. That same poster is visible when Harry first enters with Tom, and Sirius doesn't move in that shot either. However, when the poster is the focus of the shot, Sirius does move in the magical poster.
Revealing mistake: In the punch scene "replay", Harry is noticeably stockier, and I would suggest shorter, and he walks in a very unusual way - very different from Harry. Obviously a double.
Revealing mistake: When Mr Weasley is warning Harry about Black wanting to kill him there is a jug in the background supposedly magical because it is serving the drinks by itself. If you look closely you can see the wire or string or whatever held it up.
Continuity mistake: In the scene when Hermione punches Malfoy in the face, she holds her wand to his neck with her right hand. The shot changes to her turning away and then she punches him - both her hands appear in the shot and her wand is gone. In the next shot she mysteriously has her wand in her left hand with no time to have dropped it then picked it up again.
Continuity mistake: When Harry gets his turn to face the Boggart in Lupin's class, there is a wide shot showing the large clown rocking back and forth (viewer's left to right), with Lupin in the background bent over looking down at the floor. But, in the next close-up, Lupin is not as bent and is suddenly facing clown, contemplating whether or not he should do what he does next.
Visible crew/equipment: When the student's are looking at the wardrobe while listening to the teacher you can see a crew member on the glass window of the door of the wardrobe.
Audio problem: When Hermione says "I thought I just saw. Never mind" the second time, it is in a much lower tone than when she first said it.
Continuity mistake: When the Dementors enter the train, there is a shot from in the carriage looking out. In this shot there is a bottle of water on a shelf and it's moving. When the shot changes to show the carriage from the outside, the water is suddenly still.
Continuity mistake: Hagrid stands up and knocks over all of the glasses on his table at the beginning of the year. In the next shot, look to the left of Hagrid, between two candlesticks. A single glass is sitting upright on the table. In the next shot when Hagrid sits back down, none of the glasses are upright, but with the position the glass was in it should've been visible in this shot. (It's a bit hard to see, and it was spotted in widescreen.)
Continuity mistake: When Scabbers bites Ron and escapes, he and Hermione are standing very close together, but in the next shot they're further apart.
Continuity mistake: When Harry and Hermione are running from the werewolf, they hide behind a tree and start edging around it to avoid the werewolf. When they are eventually seen by the werewolf, Harry is at least a foot behind Hermione but in the next shot he is beside her.
Audio problem: Ron's "let's go" sounds different before and after the time travel.
Continuity mistake: When Sirius and Lupin cast a spell to change Pettigrew from a rat and back into human form, he is fully clothed, as was Sirius when he changed from a dog. Later, when Pettigrew changes back into a rat to escape, his clothes remain behind as he shrinks.
Continuity mistake: Hermione's blue shoes look different in a couple of scenes, from when they were walking down to Hagrid's hut compared to right after Lupin attacked them.
Continuity mistake: Hermione and Ron's feet seem really close together after Buckbeak's "execution", but after Scabbers bites Ron their feet are suddenly much further apart.
Continuity mistake: When Harry drops the Monster Book of Monsters, the scraps of torn paper are already lying around Harry's feet before the book hits the floor.
Chosen answer: Fred and George used the map to aid them in their mischievous activities at Hogwarts, and probably had little interest in what their little brother was doing or who he might be with at any given time.
raywest ★