Continuity mistake: At Hagrid's, when Harry, Ron and Hermione are there the first time in the film, there is a large birdcage, blue cup and saucer, watering can and small wood planter (with seedlings) on the windowsill. Later, when Hermione visibly throws the first stone, as the stone flies through the window the watering can and blue cup's positions differ and the wood planter and large birdcage are actually gone! When she throws the second stone they are back on the windowsill.
Deliberate mistake: In the first exterior shot through the back patio door, as the Dursleys eat, the kitchen window and patio set below are visibly quite far from the white patio enclosure. Later, when Vernon falls to the ground as Marge floats away, Petunia runs to him and now the kitchen window, on a supposed brick wall, is actually right beside the white patio enclosure. Adding to the absurdity, the entire house is in the opening shot of the film and that middle part of the wall is conspicuously missing. Additionally, even the bricks and stone top of the seat wall between the tiled patio and grass have changed.
Continuity mistake: When Malfoy and his friends bother Ron and Hermione, Harry shows up and messes with the three boys. He grabs hold of Malfoy's feet, lifts them in the air and pulls him across the snow. In the first close-up of the soles of Malfoy's boots, not a spec of snow is on them, though he was just walking in it!! Then in the next close-up, his feet still in the air, the soles are now covered in snow.
Continuity mistake: In the hospital wing, when Hermione says, "Sorry Ron, but seeing as you can't walk," the camera pans around her and Harry. BEFORE she turns the timeturner, the bed that Harry was lying in is visible and the blankets which were folded neatly in the previous shots are now off and very messy and the positions of the tall blue screen and chair near the bed are also completely different. Later, when they return, the bed is perfectly neat and the chair is pushed back again.
Visible crew/equipment: When Hermione and Harry go back in time, they duck and hide from Malfoy (after being punched) and his friends as they leave. The rectangular outline of a power pack (battery pack for hidden cordless mic) is visible at her lower back, under her pink jacket. It is visible in a few shots, including when they are at the pumpkin patch. The outline of Harry's power pack at his back is visible as well, as he bows to Buckbeak at the pumpkin patch, when they rescue him.
Continuity mistake: The actual width between the two front large wood bed posts in Harry's room at the Leaky Cauldron inexplicably changes between shots, as do their position on the wood plank floor! Here's what happens: after Harry removes his shoe and dangles it in the first overhead shot, there are five specific wood planks between the posts. Yet when he drops the shoe in the next overhead shot, there are now over five and a half wood planks between the two posts. The left post has moved to the right - by 1/2 a wood plank and the right post actually moved over one whole plank!!
Visible crew/equipment: At dinner, just after Harry takes the plate from Petunia and as Aunt Marge says, "A bit more," referring to the brandy Vernon pours, in the left glass door of the hutch behind Vernon, there is a nice clear reflection of a crew member lowering his white sleeved arm off screen.
Continuity mistake: When Harry, Ron, and Hermione are in Hagrid's hut prior to Buckbeak's execution, a stone flies in the window and strikes a pot, splitting it pretty much down the middle. There are two major shards. However, when Harry and Hermione 'relive' this moment from their position among the pumpkins, the stone (thrown by Hermione) breaks the pot in a very different pattern, with smaller pieces (and more of them). Since the same event is just being played through in time again, the pot should have broken exactly the same way both times.
Visible crew/equipment: At the end of the film when Harry is in Lupin's office, Lupin packs his bags and then he walks past his desk. He then starts saying "If I am proud..." to Harry. As he says this, he walks forwards towards Harry, passing a cabinet of skulls. Reflected ahead of him in the glass panel of the cabinet is a very large boom mic which slowly moves out of sight as Lupin walks forward. It is very visible.
Revealing mistake: Between the shots of Marge floating out of the house and later when Petunia runs to Vernon on the grass, there are many significant changes. The short brick walls that edge the Dursley garden are actually different bricks, different grout and are even aligned differently between these shots. The bushes along the wood fence are at least 2-3 ft away from the corner bricks in the first shots, but in the last shot are aligned with the corner. The height of those bushes go from being way above the top of the wood fence to being at least a foot below. In the first shots there are small metal plaques that are attached along the top of the wood fence, but in the last shot they are gone.
Continuity mistake: When Harry is in Lupin's office, as the Professor says, "I resigned..." his cane leans against the corner of the trunk beside the doorway. Yet when Harry says, "But Dumbledore..." the cane hangs off the center of the trunk. As Harry says, "None of it made any difference," the cane is actually gone, but when Lupin says, "You helped uncover the truth," the cane hangs again. Then when Lupin says, "If I am proud of anything..." the cane leans against the corner, but wait, when Lupin leaves the office the cane hangs off the trunk once again!
Continuity mistake: In the Shrieking Shack, Harry grabs Sirius Black and throws him to the floor. There are many black marks on the floorboards, like paw prints etc. Although Sirius doesn't move when Harry first throws him on the floor, the black marks on the floorboard near Black's head change between the first wideshot of him on the floor and the following closeup and in subsequent shots as well.
Continuity mistake: When Hermione and Harry hide behind the pumpkins, Hermione says, "Come on! We're coming out the back door. Go!" As HRH run out of Hagrid's, Hermione and Harry run to hide behind the trees. In the shot facing the two, with the pumpkins and Hagrid's behind them, the blanket on the ground beside the pumpkins is visible, though it is gone thereafter.
Continuity mistake: When Fred and George give Harry the Marauder's Map, Harry opens it up and on the right is Dumbledore's study. In the close-up shot of Dumbledore's study, the map is drawn with much more elaborate detail for fun and dramatic flair and the actual words of the interlocking circles are written on the map extremely differently than the previous shot.
Revealing mistake: When Ron and Hermione are arguing with Malfoy near the Shrieking Shack, Malfoy visibly flinches before he is hit by the first snowball. He's not looking in the right direction to see it coming.