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: It was a deliberate directorial decision to change the geography of Hogwarts, but it still grates with continuity. Most of the Buckbeak scenes happen around Hagrid's hut, which is down all those steps and near the forest. However in the Philosopher's Stone, Hagrid's hut is about 5 seconds walk from one of the main entrances of the school, nowhere near a load of steps and huge hill. Also, the Whomping Willow (which itself differs greatly) is on the grounds of the castle, as you see it on flat land when Harry and Ron land the flying car in the Chamber of Secrets, however in this one it is right away from the school next to quite rocky land.
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.
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.
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!!
Continuity mistake: The first time we see Hermione punch Malfoy, she turns completely away from Malfoy, then spins round and hits him. However, when Harry and Hermione watch themselves later, Hermione barely turns away from Malfoy before she punches him, and uses a different punch too. Malfoy's reaction is different as well.
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.
Deliberate mistake: When Harry drops the Monster Book of Monsters, in the first shot facing Harry's feet as the book chomps at him, he runs backwards a few steps and he stands at the foot of the bed. However, in the shot facing the fireplace, there is actually plenty of floorspace now, much more than other shots, between the rug and bed for Harry to continue to run backwards.
Revealing mistake: Just after Harry attacks Snape at the Shrieking Shack, he insists on knowing about Peter Pettigrew. In the next shot, as Lupin says, "He was at school with us. We thought he was our friend," there are wedges under the wheels of the piano, however, in the following shots they're gone.
Continuity mistake: After Hermione punches Malfoy, when he and his friends run away, Malfoy says,"Not a word to anyone, understood?" just as Hermione says, "That felt good." Then Malfoy says "jumped up mudblood" when he enters the doorway and as Ron says, "Not good," Malfoy says, "Mark my words." However, when future Hermione and Harry duck and hide, the scenario differs. As Malfoy and friends run, he says everything, "Not a word to anyone, understood?" through "jumped up mudblood. Mark my words," and that's when Hermione says, "That felt good."
Revealing mistake: While Hermione and Ron watch, cloaked Harry starts up with Malfoy and his two friends as they all stand in the snow. Most noticeable in the wide shot, when Harry spins the Slytherin boy, although the boy's feet visibly disturb the snow, Harry's feet do not make a mark - no footprints whatsoever.
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.
Factual error: In the scene immediately following Harry and Hermione's travel back through time, she tells him, "It's 7:30." The clock, however, is striking the bells for an hour, not a half-hour.
Continuity mistake: In Harry's room at the Leaky Cauldron, the rug and log holder's positions change. For instance, in the shot from under the bed, as Harry's head looks upside down at the Monster Book of Monsters, the rug in front of the fireplace is directly ahead. The right edge of the rug is aligned with the bed post on the wood floor. However, in the shot from the top of the bed the rug's position is now much farther to the right, use the wood planks as a guide.
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.
Visible crew/equipment: When Harry and Hermione are at Hagrid's to rescue Buckbeak, Harry walks toward the hippogriff and bows. In the next shot just as Beaky bows, when his head is down low, look directly in between the right edge of the screen and the wood post, above the pumpkins. A pair of black pants quickly pass to the left; it's certainly not one of the crows, unless it grew human legs. (Only visible in widescreen.)
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.