Continuity mistake: In the CoMC class, when Hermione says "I think they're funny", you can see her Time-Turner outside her robes. When she turns to look at Malfoy, it's not visible anymore.
Continuity mistake: When the executioner goes to chop the pumpkin (the second time), you see Fudge reaching for a crow on his hat. In the next shot, both his hands are at his side.
Other mistake: When Fred and George pass on the Marauder's Map to Harry, we see the map start to reveal itself. As it does Harry starts to read "Messrs Mooney, Wormtail, Padfoot and Prongs." Harry reads the word Messrs before it even appears on the page.
Continuity mistake: When Harry and Hermione are back in time and hiding in the woods. Notice that Hermione has a bruise/sore on the bottom corner of her lip that keeps appearing and disappearing.
Continuity mistake: In the Time-Turner scene, when Hermione says, "Malfoy's coming," it shows her starting to jump through the archway before Harry. In the next shot, it shows Harry coming through first.
Continuity mistake: When Harry is about to pass out and says "Sirius", he says it in two breaths (Siri-us). The second time, when Harry and Hermione are watching this same exact scene occur in time, he says it in one breath (Sirius).
Audio problem: The song "Something Wicked This Way Comes" is staged with a mixed choir, with a majority of girls. However, to the trained ear, you can tell the song is sung by an all-boys chorus.
Continuity mistake: The position of the "little old lady at twelve o'clock" in comparison to the bus while she's crossing the street changes quite a few times.
Revealing mistake: The first time the bus conductor shows Harry the newspaper with the picture of Sirius Black on the front, one of his fingers disappears "underneath" the moving picture for a split-second.
Continuity mistake: The first time Harry, Ron, and Hermione leave Hagrid's hut before Buckbeak gets "executed," Hermione opens Hagrid's back door and all three are peeking out of it before Hagrid opens his front door. The second time, when Harry and Hermione are watching from the pumpkin patch, Hagrid opens the front door at about the same time that Hermione opens the back one, and Ron and Harry aren't even seen yet. Because this is the same event in time from two different points of view, it should be absolutely synchronized.
Revealing mistake: When the students are running towards the portrait of the hippos where the Fat Lady is hiding, watch the railing of the stairs. It shakes back and forth, showing it isn't really made of stone.
Continuity mistake: When Snape and Harry are in the hallway and Lupin shows up and Snape goes, "Well, well, Lupin," you see Harry in the background attempting to tuck away the Marauder's Map in his pocket. When Snape grabs for it, he reaches up more, as if Harry is holding it more by his shoulder.
Continuity mistake: When Ron drops Scabbers after Buckbeak has been 'executed', he and Hermione are very close together, note the position of their feet. In the next shot, when Ron says, "He bit me," Hermione is now standing farther away from him.
Other mistake: During the whomping willow scene, Hermione does indeed say Rupert, not Ron. She says it quickly, but I am not the only one who hears her say Rupert. She definitely does say Rupert. I just listened to it 3 times to make sure. [This may differ between versions - people are equally convinced on both sides.]
Continuity mistake: In the "Care of Magical Creatures" scene, Hermione gets a fright and there is a close up of her grabbing Ron's sleeve. From a different shot seconds later, you can see her grab his sleeve again in the distance.
Continuity mistake: Just after Ron pushes Harry toward Buckbeak, the hippogriff is seen defecating. In shots after this, the hippogriff's droppings have altogether disappeared.
Continuity mistake: After rescuing Sirius, Harry and Hermione return to the hospital wing as the bell starts to chime. They make it up there before the bell is done, despite having to run up at least five stories. Don't you think that's a bit too fast?
Revealing mistake: During the Knight Bus scene, Harry smacks into the glass twice. Both times this happens, it's the same shot used twice.
Audio problem: When Cornelius Fudge says, "Oh yes, indeed, indeed." near the end of the movie, his mouth doesn't move.
Continuity mistake: During the scene in which Uncle Vernon's sister Marge is turned into a balloon we see her floating out of the conservatory. A second before she is blown out the door we see from the shot looking into the conservatory that Aunt Petunia is to the right of the conservatory doors inside the dining room. When the shot changes, she is now standing in the doorway to the conservatory.
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 ★