Continuity mistake: When Harry, Ron and Hermione first exit Hagrid's cabin to get away from the ministry, they wait a lot longer at the door before running away, than when Harry and Hermione go back in time. (01:22:20 - 01:47:25)
Continuity mistake: Outside Hagrid's when Cornelius Fudge says, "...shall be executed this day at sundown." you see Harry, Hermione and Ron hide behind some pumpkins. You can also see a crow standing on a pumpkin right in front of them. When it cuts from behind them that crow is gone. (01:22:45)
Continuity mistake: The first time we see Dumbledore tell the executioner his services are no longer required (in a shot from the stone circle), he lifts his staff and points at him. The second time (in a shot from the pumpkin patch), Dumbledore does not lift his staff. (01:23:25 - 01:50:30)
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." (01:23:30 - 01:49:50)
Visible crew/equipment: In many shots throughout the film, there are noticeable reflections of either the reflector screen or studio/set lights, in the lenses of Harry's glasses, as well as Professor Trelawny's. (01:24:00)

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 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 gone. When she throws the second stone they are back on the windowsill. (01:24:05 - 01:52:20)
Continuity mistake: At Hagrid's, when Harry, Ron and Hermione visit the first time, the quilt lying on the chair changes position over and over again, from lying over the back of the chair, to being on the seat and so forth, until Hagrid takes it to cover his little creature. (01:24:35)

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. (01:24:45 - 01:51:15)
Continuity mistake: At Hagrid's, after the jar breaks the first time, in the wide shot the toad is on the table, under the cracked pieces of jar, yet in the next close-up, the cracked pieces are gone and the toad is back on the blue plate. Later, when Hermione throws the stone, the toad is on the plate (which is farther from the jar now) as the jar breaks. (01:24:50 - 01:51:20)
Continuity mistake: When the stone hits Harry, the very first time, in the shot inside Hagrid's, he yells, "Ow!" and as he turns the blue cup touches the wood tray. In the next exterior shot, the blue cup is closer to the birdcage. (01:24:55)
Continuity mistake: When Hermione and the others are in Hagrid's hut, a rock with a swirl on it hits the pot. Later, when Hermione and Harry are reliving the scene from the exterior view, Hermione picks up the "same" rock to throw at the pot. The rock is different though, it has a bigger swirl on it. (01:24:55 - 01:51:15)
Revealing mistake: After Ron has been dragged down the hole by the Grim, you see both Harry and Hermione get hit by The Whomping Willow and they fly backwards and land on the ground. Notice when Harry places his left arm in the ground, the ground is unnaturally soft. (01:25:00)
Audio problem: At Hagrid's, as we are hearing Fudge's voice saying, "The Hippogriff known as Buckbeak, hereinafter called the condemned, shall be executed..." it is actually Hagrid that we see talking, as we see them standing at the window. (01:26:00)

Visible crew/equipment: When Dumbledore, Fudge, and the executioner show up at Hagrid's hut (the first time), Harry, Hermione, and Ron sneak out the back then hide behind the pumpkins, and the mic pack bulge can be seen under Hermione's hoodie, at her side. (01:26:10)
Continuity mistake: When Harry, Hermione, and Ron are hiding behind Hagrid's pumpkin patch in an attempt to hide themselves from Fudge and Dumbledore, Hermione turns around at the sound of a 'crack' in the forest, she then turns to her left and runs with the others. Later, when seen from Hermione's view reliving the past, Hermione at the pumpkins turns to her right before running with the others. (01:26:20 - 01:52:20)

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. (01:27:25)
Continuity mistake: When Sirius, Lupin, Snape and the rest are gathered together in the Shrieking Shack, in some of the shots we see the main double doors swing back and forth, due to light gusts of wind. However, the doors' positions instantly change in some consecutive shots, even though there is no wind between the two shots. (01:27:35 - 01:30:45)
Revealing mistake: While he sits by the Whomping Willow, Ron shouts, "Harry, Hermione, run! It's the Grim!" When Sirius the dog runs toward them, in the shot facing Harry and Hermione, their eyes are not quite in sync with the dog before it leaps. (01:28:00)
Audio problem: As Sirius, the dog, drags Ron towards the Whomping Willow, Hermione and Harry chase after them. When Sirius actually backs up into the hole below the tree trunk, Ron begins to shout, "Help!" In the next shot, as Harry starts to stretch his arms forward to dive down, Hermione runs behind him and visually she shouts Ron's name, though there is no sound heard. (01:28:15)
Continuity mistake: In the Shrieking Shack, Snape enters the room brandishing his wand at Lupin and Black, and both Lupin and Black back away from Snape. Lupin and Black both lean back on the big piano that's in the room. Yet when the shot changes Lupin is still backing away from Snape, and neither Black or Lupin are in front of the piano, let alone leaning back on it. (01:29:20)
Chosen answer: It's not known what it is. It is left to the audience's imagination of what exactly is in the room or what some witch or wizard was doing in there. This is only meant to be a humorous bit and is unrelated to the plot. It didn't happen in the book.
raywest ★