(at around 12 mins) When Harry receives countless acceptance letters from Hogwarts, he fights with Uncle Vernon, saying the dialogue "They're my letters! Let go of me!" Harry's voice is far deeper than the Harry in the rest of the movie, indicating this line was re-dubbed long after main production when Daniel Radcliffe's voice had already begun to change. (Also, his lips are not moving when he says those lines.)
(at around 1h 11 mins) When Harry and Ron are fighting the troll in the girl's toilet, they use a spell to lift the troll's club over its head and drop it. The club does hit the troll and makes an appropriate sound effect, but when the club falls to the floor, it makes no sound at all.
Owls are very quiet in flight. They have to be, they are hunters and rely on being able approach their prey silently and hear where that prey is in the first place. The owls in Harry Potter - especially in the scene where hundreds of them gather outside the Dursleys' house in Privet Drive - are very loud. Every time they appear, the soundtrack contains loud flapping noises which sounds more like some sort of pigeon than any owl.
(at around 1h 12 mins) In the scene following the defeat of the troll, Quirrell is shown speaking with the other professors, at which point they, and the trio, leave the girls' bathroom. Their footsteps are clearly heard as they move down the hall; however, in the next shot of the troll laying on the floor, the sound effects have ceased. In the last shot, of Quirrell jumping nervously in response to the troll grunting, the footsteps can again be heard.
(at around 35 mins) Twice in the film, the British word "bogey[s]" is spoken: once when Harry and Ron meet on the train, and once at the end of the troll scene (at around 1h 12 mins). On the American DVD, the subtitles transcribe this as "booger[s]", a synonym which sounds very different.
(at around 48 mins) When Percy is taking the first years to Gryffindor Tower, they all seem excited by the idea of moving pictures, even though most of them would have come from magical families and moving pictures would be perfectly normal to them.
(at around 44 mins) In the sorting ceremony scene, Ron goes up to get sorted into his house. After being put into Gryffindor house he runs off in the direction of the tables on the left side of the Hall, even though we know that Gryffindor house table is on the right side.
(at around 7 mins) When Dudley falls into the snake pit and the glass reappears, by looking at the expression on his face he is calm so we can tell he thinks that there is no glass. He then puts his hand against the window and then gets scared. If he didn't expect glass he wouldn't have put his hand against the window.
(at around 40 mins) When Harry arrives at Hogwarts, Professor McGonagall announces that the Sorting Ceremony will begin "momentarily". In UK English, momentarily means "for a moment" (i.e. briefly), and a Scottish witch as pedantic and precise as McGonagall would never use the American meaning of the word ("in a moment" or "soon"), even though the American meaning might be well understood. Then again, given that the otherwise equally pedantic Snape says "less" when he means "fewer", it could just be that the teaching staff's use of English is just as sloppy as it is in schools all over the Muggle world.
(at around 46 mins) After Harry gets sorted into Gryffindor he goes and sits down next to Ron with Hermione across from him who is sitting next to Percy. In the next shot when Harry asks who's that teacher next to Professor Quirrell he asks Percy and Hermione is sitting to the right of him and Ron is across from him.
(at around 1h 29 mins) When Harry is in the restricted section, he sets down the lamp to his left before taking off his invisibility cloak, setting the cloak to his right. When Filch's voice is heard and Harry grabs the cloak, the lamp is on top of the cloak and thus falls onto the floor.
(at around 2h 20 mins) During the end of the film, as the train starts leaving Hogwarts, you can see that Hagrid is a little bit taller than the train. In the next camera shot, Hagrid is shorter than the train.
(at around 20 mins) In Diagon Alley, Harry and Hagrid pass many groups of people multiple times, though they appear to be walking continuously in one direction. Watch for the wizard with curly red hair, the man with a top hat and mutton chops, and the group of three girls who cross in the foreground of the opening shot.
(at around 1h 29 mins) When Harry goes looking for a book on Nicolas Flamel in the restricted section he opens up the screaming book to the first page. When the book starts to scream he is in the middle of the book.
(at around 21 mins) Just after passing Madam Malkin's shop and before the owl emporium in Diagon Alley, a woman dressed all in black and a man with a burgundy top hat and mutton chops pass on Harry's right walking in the opposite direction. In the next shot, as Harry looks to his left, the same pair can be seen standing and chatting in the doorway of the owl emporium.
(at around 11 mins) When Mr. Dursley is talking about how there's no post on Sundays and the first letter shoots out of the fireplace, the log poker is in the middle of the hearth, when all the other letters come shooting out, the poker is on the right side.
(at around 1h 10 mins) When the troll attacks Hermione the first time, its club demolishes the first three stalls. Right before the troll swings its club again, the door of the second stall is still standing.
(at around 52 mins) When Harry is writing down what Snape is saying, the writing is clearly different in the close up shot, than every other time we see the paper, it is much larger and messier whereas in the close up it is small and neat.
(at around 1h 15 mins) When the Gryffindor team are walking to Harry's first Quidditch match, behind Harry, in the light, is a girl with blonde hair. But when they are under the wooden shelter she has become a girl with brown hair.
(at around 21 mins) In Diagon Alley, Harry and Hagrid walk past the same cart and storefront three times. In the opening wide shot, they walk past the purple storefront with the yellow moving scissors and the cart of market goods in front of it. Three shots later, the storefront and cart are shown again in detail, as Harry and Hagrid pass. The next shot shows them passing the cart (with a stack of cauldrons in the background). Several shots later, after passing the store with the owls, they are seen once again passing the cart with the same stack of cauldrons in the background.
(at around 14 mins) In the hut on the rock, when Hagrid comes to fetch Harry, Harry's T-shirt is hanging off his left shoulder at the beginning of the scene, and then it is in the center of his chest, then hanging off the left again, and then back to center.
(at around 13 mins) When the shotgun blast from Vernon's shotgun goes off he only pulled the trigger one time. But when the hole in the ceiling is seen there are two partial holes seen side by side. A double-barreled shotgun has two triggers so that the blast doesn't knock the shooter back on their rear end. Therefore there should only be one hole in the ceiling.
(at around 46 mins) When Harry has been sorted into Gryffindor, he goes to sit next to Ron, opposite Hermione, but when the meal begins, he is sitting next to Hermione. He is also on her left-hand side, away from the top table; this would imply that he was sorted before Hermione, instead of afterward.
(at around 2h) In the chess sequence the White (enemy) Queen is shown destroying 2 separate Black Rooks, but as Hermione took the Queen side castle there would only be 1 Black Rook piece in play. It is possible that a pawn was promoted but as it is shown on screen that Black (Team Ron) loses their Queen they would likely replace it with a Queen making this unlikely.
(at around 10 mins) When Harry peers out from under the stairs Uncle Vernon is screwing a board over the mail slot. The board in this shot runs from the upper right of the screen to the lower left. But in the shot when the letters start flying into the house the board is positioned from the upper left to the lower right.
(at around 2h) In the chess sequence, Harry is shown on a3 as a Black Bishop when Ron moves to h3 to check the King on g1 before being taken by the Queen on c3. Given that Harry moves to check the King his only possible move would be to go to c5 which would not be checkmate, making Ron's sacrifice in vain as the King is free to move to f1 or g2 since Hermione is on h8. A cheating spell may have been employed.
(at around 35 mins) After Harry has bought the contents of the sweet trolley on the train, an exterior shot shows that the sun is still fairly high. Hermione then joins them, and tells the boys that they had better change into their robes as they will be arriving soon. Yet when the train pulls into the station it is at night.
(at around 5 mins) When Harry and the Dursleys are getting into the car before going to the zoo, Vernon is seen speaking to Harry. From the backside, Harry's button up plaid shirt is seen on his shoulder, then from the front it is hanging off his shoulder.
After their shopping trip to Diagon Alley, Harry and Hagrid have supper in the Leaky Cauldron. A camera shot from up above clearly shows, that they are alone in the room. Cut to Harry, and behind him are two people sitting at a table that was vacant a second ago.
(at around 32 mins) Hogwarts students reach the train by going through King's Cross Station platform no. 9¾, which is secretly located in the barrier between platforms 9 and 10. In reality, platforms 9 and 10 are in separate buildings, and there is no barrier between them, but railway tracks. People wrote to J.K. Rowling about this, and she admitted getting confused between King's Cross and Euston stations. The Platforms actually used in filming are platforms 4 and 5.
(at around 34 mins) Harry and Ron first encounter each other on the platform at King's Cross station, yet on the Hogwarts Express, when Ron asks Harry if he can share his compartment, mountains can be seen out of the windows. This could not be until at least a couple of hours after leaving London. Why did it take Ron so long to find a seat?
(at around 1h 30 mins) When Harry, wearing his Invisibility Cloak, sees Filch looking for him, then spies on Professors Quirrell and Snape arguing, the shots filmed from Harry's point of view have him at eye level with the adults even though he is clearly shorter than they are.
(At around 1h 6 mins) Wood tells Harry that, if he catches the Golden Snitch "... the game is over" and "...we win." This is only partly true. Catching the snitch will end the game, but the team with the most points at that time is still the victor, regardless of who catches the snitch.
(at around 12 mins) When Harry is lying on the floor of the hut, drawing a birthday cake and waiting for his birthday to begin he watches Dudley's wristwatch which turns from 11:59 to 12:00 which it would only do at noon. At midnight it would turn to 00:00.
(at around 1h 45 mins) In one scene, Hermione calmly says the word "Voldemort" without the customary flinch or shudder. However in all future scenes and sequels, Hermione is clearly reluctant to say the name and does not overcome this fear until Harry Potter and the Order of the Phoenix. However, as Hermione is Muggle-born and is still young, it is possible she does not yet know the full significance of the name.
(at around 50 mins) When Ron and Harry come into Professor McGonagall's class late and she transforms from a cat into a human, she is not wearing glasses at first, yet they appear on her face as she turns to address the boys. This effect is on purpose. She is transforming between cat and human as she approaches the boys and her glasses are the last thing to reappear.
When Wood is showing Harry the Golden Snitch, after it is released for flight he is shown looking elsewhere and not where the Snitch is. Although this might be seen as a mistake, it is actually intended to give the impression that only a Seeker is skilled enough to follow the flight of the Snitch which Wood had described as "Small, wicked fast and damn near impossible to see". While Wood, the Gryffindor teams Keeper is not able to find the flying Snitch, Harry as the teams new Seeker is easily able to see it.
The number of place settings at the tables at the initial feast show that there are 8 first-years in each house, which would make 32, but when the pupils are lined up for their first flying lesson, there are only 26. However, it's perfectly reasonable to have extra place settings at the house tables - regardless of the total number, it isn't known how many first-years will be seated at each table until they are sorted.
Although moving and talking portraits are a hallmark of the Harry Potter universe, not all wizarding portraits are like this. We see many ordinary, non-moving portraits at Hogwarts throughout the film.
(at around 56 mins) When the students are first learning about brooms, Madam Hooch tells the students to kick off from the ground once she sounds her whistle. She blows her whistle and Neville starts to rise from the ground. Even before he loses control of the broom, she yells at him. He's the only one who did as he was told. Why is he in trouble?
At the end of the film, Harry says, "I'm not going home. Not really." This line is not in the book because it would create a severe plot hole. Lily's charm, completed by Petunia and reinforced by Dumbledore, ensures that the Dursley's home would remain safe for Harry and hidden from Death Eaters for only as long as he can call it home. If he truly felt that Hogwarts was his home instead of his Aunt's house, the protective spells would break.
After Harry leaves the library, having been heard by Filch, he goes down a hall and hidden under his cloak he encounters Profs. Snape and Quirrell. While standing there, Filch comes up and reports to Snape and Quirrell, "There's a student out of bed." He, Snape, and Quirrell take off to find the offending student. Harry then goes off and finds the Mirror or Erised, goes back to the dorm and gets Ron. Yet neither is caught out of bed.
Before the Qudditch match Madam Hooch tells the Gryffindors and Slytherins she wants fair play from both of them. But Slytherin clearly disobey as they knock out Oliver Wood and Angelina Johnson on purpose.
At the beginning of the movie, when Harry Potter is dropped on the doorstep of the Dursleys (after his parents' death), he is clearly an infant. However, in the album that Hagrid gave Harry at the end of the movie, there is a picture of Harry as a toddler with his parents. If at the beginning of the movie he was an infant when he was orphaned, then it is not possible for him to have a picture with his parents when he was a toddler.
(at around 54 mins) When Harry is reading aloud the article in the Daily Prophet about the break-in at Gringotts, he reads words that are not in the article. In particular, he says, "The vault in question, Number 713, had in fact been emptied earlier that very same day." The words "Number 713" do not appear on the page. Harry would have then been unable to connect this to the vault he and Hagrid visited at Gringotts.
(at around 1h 40 mins) [extended version only] When Harry is reading about Nicholas Flamel on the back of Ron's Dumbledore card, the lime green can clearly be seen where Dumbledore's picture is supposed to be.
(at around 17 mins) In the hut on the rock when the Dursleys panic after Hagrid grows Dudley a tail, Hagrid is played by Martin Bayfield not Robbie Coltrane. The same can be noticed in The Leaky Cauldron when Hagrid enters the building.
(at around 2h) During the chess scene when the chess pieces are being destroyed, the bits of rubble can be seen flying in opposite directions and sometimes even just a split second before the actual piece is destroyed.
(at around 1h 1 min) When Harry, Ron, and Hermione are walking up the stairs and the stairs are changing, you can still see the banister wobbling back and forth even after they've reached their final position.
(at around 11 mins) When the multiple letters fly into the house from the fireplace, Harry catches one out of the air and it is obviously a single sheet of paper rather than a stiff envelope like the first one that was delivered and opened.
(at around 28 mins) After Harry has received his wand in Ollivander's, his hair is parted to show his scar. However, when Hagrid knocks on the window and Harry sees Hedwig, his scar has mysteriously disappeared.
(at around 1h 1 min) When Harry, Ron and Hermione first enter Fluffy's corridor, and start running towards the door, one of the torches clearly has a little flame, before it 'bursts' into flame when they pass it.
(at around 54 mins) There are two articles on the front page of the Daily Prophet about the break-in at Gringotts. The article below the headline story, starting with the line "the vault in question had in fact..." is identical to the top article.
(at around 51 mins) When Snape first enters his classroom, he bursts into the room and the door slams open. The actor who is sitting in the front row on the right continues to look at the door well after Snape has made his way to the front of the class, as if expecting the door to close. He also does a double take during this time.
When Draco Malfoy is being sorted, the Sorting Hat calls out "Slytherin" before it is actually placed on his head, which is pretty much the way it happens in the book. However when Professor McGonagall lifts the hat away from his head, his hair is clearly out of place as though the hat had actually been sitting on his head.
The goof items below may give away important plot points.
(at around 1h 35 mins) Hagrid tells the trio that Professor Snape helped put forth protections over the stone; therefore, he could not possibly be trying to steal it. However, Snape's contribution from the book - a logic puzzle involving a number of different potions - was left out of the film and not given a replacement, making Hagrid's statement invalid.
(at around 44 mins) When Harry sees Snape in the Great Hall during the sorting ceremony, we can see the back of Professor Quirrel's head. Quirrel's hair is clearly visible under his turban despite the fact that Voldemort's head would be here. It is gone when Voldemort is revealed.
After escaping from the Devil's Snare, Harry, Ron, and Hermione all have dirt stains on their faces and clothing (from landing in the dirt beneath the plant). The amount and placement of the dirt stains vary from shot to shot throughout the finale, and in some shots seem to disappear entirely. This is most noticeable on Hermione's tights (the white provides a strong contrasting background for the dirt).
When Harry first meets Professor Quirrell, his scar doesn't hurt even though it did every other time Quirrel was near. It has been confirmed by JK Rowling that Voldemort did not 'possess' Quirrell until after the break in at Gringotts, so at Harry and Quirrell's first meeting he did not have Voldemort sharing his body.
(at around 2h 10 mins) After the final fight when Harry is lying unconscious his hair is thrown back revealing his scar. It has clearly been drawn on with a marker and looks much less real than the wounds on his cheek.