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 then the club falls to the floor, it makes no sound at all.
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.
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.)
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.
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. On the American DVD, the subtitles transcribe this as "booger[s]", a synonym which sounds very different.
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.
In the scene where Ron and Harry are late for Professor McGonagall's class and she is a cat, when she transforms back to a human, her glasses are not on her face, when she turns to face the boys, they just appear on her face.
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.
In the sorting ceremony scene, Ron goes up to get sorted into his house. After being put into Gryffindor house he runs of 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.
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.
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.
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.
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.
In the scene in the hut on the rock, where 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.
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.
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.
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.
In the scene where 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.
In the scene where 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.
During Charms class Seamus blows up the feather, and it can be seen floating down, and lands. When Harry says "I think were going to need another feather over here professor." It can be seen coming down a second time.
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.
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.
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.
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.
When the Gryfinndor 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.
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.
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?
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.
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.
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 (2007). However, as Hermione is Muggle-born and is still young, it is possible she does not yet know the full significance of the name.
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?
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.
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.
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.
When Aunt Petunia is cracking the eggs and finding they are filled with letters rather than yolks, the envelopes are clearly a thin sheet of paper, not a thick envelope with a letter inside. (You can tell they are envelopes because you can see one is addressed the same as the previous envelopes)
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.
In the scene 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.