(at around 17 mins) When Harry first meets Hermione in Diagon Alley, she casts a spell that fixes his broken glasses. (Arthur Weasley did this in the book.) Underage wizards/witches aren't allowed to use magic outside of school, yet Hermione isn't prosecuted. In a heavily populated area, it's impossible to trace any spell to a specific person.
(at around 35 mins) In Professor Lockhart's first lesson, he mentions that he 'didn't get rid of the Bandon Banshee by smiling at him.' Banshees are always 'her', not 'him'. The book got this right, but the film changed it to make Lockhart look even more like an idiot.
(at around 3 mins) When Dobby starts to cry and goes to jump off the bed, Harry's eyes follow him, but don't keep up with his speed. The on-set puppet Dobby was not as fast as the CGI Dobby that was added in later.
(at around 1h 5 mins) When Snape uses "Expelliarmus" on Lockhart, he is thrown through the air and still has his wand in his hand afterwards. The spell is supposed to make the opponent lose their wand and it is very unlikely that Snape would fail to perform the spell correctly.
(at around 1h 9 mins) When Ron and Hermione inform Harry he is a Parselmouth, he says, "I know. I mean I accidentally set a python on my cousin Dudley once". But the snake that escaped in Harry Potter and the Sorcerer's Stone was a boa constrictor.
(at around 9 mins) When the three Weasley brothers come to rescue Harry, Harry says 'Ron, Fred, George' in that order. The twin in the back of the car nods in response to the name Fred, however this is Oliver Phelps, who plays George. Seconds later, Ron tells Fred to drive and the twin behind the wheel (James Phelps) correctly responds.
(at around 22 mins) At the end of the confrontation between Lucius Malfoy and Mr. Weasley in Flourish and Blotts, Lucius Malfoy says, "See you at work," to Mr. Weasley, but Lucius Malfoy doesn't actually work for the Ministry of Magic.
(at around 1h 50 mins) When Harry and Ron are in the car being chased by the spiders, Ron switches gears with Harry's hand over his. The clothing sleeves shown on them in that brief shot are not the clothes they're wearing in that scene, but what they'd worn in the earlier flying car scene at the beginning of the movie.
(at around 48 mins) During Professor McGonall's class where in she discussed about the history of the Chamber of Secrets, Crabbe, Goyle and Draco Malfoy can be seen wearing a different colored necktie (just the like Ravenclaw's) than their house.
(at around 34 mins) Ron receives the "Howler" from his mother. After his owl, Errol, crashes into the table, you can see that the red envelope is open. As Ron removes it from Errol's mouth. We then see Ron breaking the seal on this envelope so he can read it.
(at around 1h 5 mins) When Professor Lockhart is knocked backwards by Professor Snape's charm during their duel, his wand can be seen flying through the air. When he lands, however, the wand is back in his hand.
(at around 57 mins) When Harry breaks his right arm playing Quidditch, he takes great care to keep it held up as he rolls from side to side to avoid the bludger, but at one point he puts his weight on it without any apparent discomfort. In the next shot he is holding it across his stomach again.
(at around 15 mins) When Harry is in Borgin & Burkes in Knockturn Alley, he approaches the glass dome with skulls sitting on the shelf and to the right is a large round mirror sitting atop a cabinet. When he walks away after freeing his hand from The Hand of Glory, in this wide shot there is now a very tall, ornate, wrought iron fixture behind him that stands beside the shelf, in front of the round mirror and cabinet, that was not in that previous shot.
(at around 1h 8 mins) In the duel scene between Harry and Draco, Lockhart walks in front of Harry to cast his spell on the snake. Lockhart is standing between Harry and the snake, though when the snake lands, Lockhart is far behind Harry, back in his original position.
When Harry accidentally travels to the Dark Arts store (Borgin and Burkes), his glasses are cracked when he exits the fireplace. When Harry comes out of the coffin from hiding, his glasses appear to be intact. In the next shot, they are cracked again.
(at around 1h 20 mins) When Harry, Ron, and Hermione are drinking the Polyjuice Potion, Harry leans toward the mirror and starts to gag. His shirt is half-unbuttoned. A few frames later, his shirt is buttoned up, nice and neat.
(at around 11 mins) When Harry is looking at the "clock" after arriving at the Weasley's, it shows Ginny is in the garden with the her mother. However, she comes running down the stairs a few minutes later, meaning her picture should have been under "Home" instead.
(at around 2h 15 mins) When Harry starts destroying Tom Riddle by drilling his diary with the Basilisk's tooth, Riddle is visible acting with two empty hands. In the next two shots featuring him, he is obviously holding Harry's wand in his right hand. Afterwards, his hands are empty again, when in the final shot, where Tom disappears completely, the wand is lying on the floor beside Dumbledore's hat.
(at around 1h 19 mins) As Ron and Harry watch in the background, Crabbe and Goyle hold cupcakes that change position, then start eating Hermione's cupcakes. When the close-up faces Crabbe, the little bit of cupcake in Goyle's hand is visible. However, when Goyle rolls his eyes up as he begins to fall backwards, the cupcake in his hand is nearly whole.
Throughout the film, one of the young actors may have one or more pimples on their face, yet in the following shots which may take place only moments later, the pimples are gone, or visa versa. For example, when Hagrid joins Harry, Hermione and Ron outside when he overhears, "Mad and hairy...," Harry has one on his cheek. Neville tells them to rush to Harry's room. While Harry, whose own pimple has disappeared, searches the mess, the one on Ron's chin is visible, though it wasn't in the shot outside. Scenes are shot out of sequence, hence the erratic complexion continuity problem.
(at around 27 mins) When Harry and Ron's car is caught by the tree, a limb smashes a hole in the rear window but the hole is missing in one shot when the car tips forward while falling out of the tree.
(at around 27 mins) While in the Whomping Willow, the center point of the cracks and spider cracks around it on the car's windshield changes shape and position. In the first shot of the windshield being smashed to four shots later of Harry turning towards the back, with the windshield visible behind him. Regardless of whether more damage occurs to the windshield, the center point of each of the two cracks should be in the same place, which it is not.
(at around 54 mins) During the Quidditch match, just after the close-ups of Snape and Lucius Malfoy, there is a shot of Harry flying towards the camera, coming to stop, with Draco Malfoy flying in beside him and in this shot the goal posts cast a shadow on the sand. Malfoy remarks, "All right there, Scarhead?" and Harry looks down below at the approaching Bludger. Now in this shot, not only do the goal posts have a completely different shadow, there are no hoops at the top of the poles' shadows (while the angle might make them hard to spot, putting everything in a line, the shadows should at least thicken at the top where the hoops are).
(at around 1h 19 mins) In the girls' bathroom, immediately after Hermione says "add the hairs", Ron can be seen with an empty hand. In the next shot, he is putting the hairs into the glass with that same hand.
In the Whomping Willow, the trunk of the car receives a noticeable gash just above the lock on the trunk as well as a huge dent in the trunk. However just before the trunk pops open to eject Harry and Ron's belongings, it is blatantly apparent that it is not the same car trunk. The gash and dent are both gone, the Ford Anglia nameplate on the right side is gone, the lock is different, the area under the bent fender is different, etc. After the spider escape, though the nameplate is back, the dent and gash are still gone.
(at around 26 mins) During the car flight on the way to Hogwarts, Harry and Ron have gone out of control outside Hogwarts. When the car is approaching the whomping willow, the car is massively out of proportion compared to when the car is in the tree.
(at around 28 mins) Harry and Ron's trunks are being thrown out of the car and in the shot just before Harry's close-up, Ron's trunk (the other trunk says HP) slams down on the grass. The top of this trunk has a large perfectly symmetrical hole in the center with four round marks around it, which was probably involved in the throwing somehow. In the wide shot as Hedwig is being tossed out, the trunks are clearly visible and there is no hole in either, nor is there a hole in Ron's trunk at any other time.
(at around 57 mins) As Harry chases the Snitch after his arm is broken, he reaches and catches it in the shot facing him. In the next side shot, as he begins to roll over while still balancing on top his broom, the attached foot rest is visible between his thighs. However, when he rolls under his broom then skids to the ground, it is clear that the foot rest is gone. Whether the foot rest is in the open or closed position, it would still be visible either above or below his leg.
(at around 24 mins) At all times the Locomotive 'Hogwarts Express' is played by a Great Western Railway Hall Class Locomotive. However, when Harry and Ron are in the car and look behind them to see the train bearing down on them the front of the engine is quite different, although the numberplate and nameboard are the same.
(at around 6 mins) When Harry is chasing after Dobby in his house and they get to the downstairs hallway they both stop running. Harry stops and he has one leg in front of him. In the next shot, the other leg is in front of him instead.
(at around 1h 45 mins) When Harry and Ron are in the car trying to get away from the spiders, Fang gets into the car twice. Then he is alternately sitting down, standing up, leaning forward, and looking out the back window between shots.
(at around 22 mins) When Harry's cart hits the barrier between platforms 9 and 10, Hedwig's cage door very clearly pops open. In the next shot she is shown ruffling her feathers with a very closed cage door.
(at around 9 mins) There are eleven vertical front bars on Harry's window, five on each side of the center bar. Ron hangs the hook to the bars on Harry's window and when he says "Let's go!" we see the hook between the third and fourth bar on the right. Yet in the next shot and also in the shot looking up as the bars fall, the hook is between the fifth and sixth from the right.
(at around 25 mins) As they fly over Hogwarts Express Ron yells, "Take my hand!" the corner rubber trim of the door frame is peeling up. When Ron grabs hold in the shot facing Ron, their hands are positioned differently than in the next close-up where it's visible that the frame of the door is fairly clean, there are two parcels behind the seat, etc. Yet when Ron grabs hold after Harry says, "...Your hand's all sweaty," the rubber trim is fitted into place, the frame of the door is filthy and there are different parcels behind the seat, etc.
(at around 1h 45 mins) As Aragog approaches Harry and Ron, Harry says, "We're friends of Hagrid's," and Harry carries the lantern palm side up, at his hip. Yet in the next shot, it's palm side down and the lantern handle is at his shoulder. In the next shot, though it's still at his shoulder it's palm side up now. Then in the two shots facing Aragog, the lantern is down low, but in between those two shots, in the shot facing Harry, his elbow is bent, the lantern is higher up and Fang stands further away.
(at around 22 mins) As Ron's luggage trolley slams into Harry's, Ron's trunk is visible. As Ron begins to flip over in the overhead shot, the trunk has five strips of brown trim - two on the edges and three in the middle. When Harry and Ron moan and get up, Ron's trunk now has four strips of brown trim - two on the edges and two in the middle.
(at around 27 mins) When in the Whomping Willow, Ron asks, "What's happening?" and Harry replies, "I don't know." After a few other shots, in the next two front close-ups of the boys as they scream, Harry, Ron and Hedwig are not alone in the car. A crew member's hand is quite visible holding the bottom of Hedwig's cage and in the 2nd close-up is actually laying the cage on its side.
(at around 1h 48 mins) When Harry and Ron are in the car fleeing from the spiders, there is a close-up of them looking towards the back of the car as they drive backwards. Two shots before the close-up of them yelling, "Wooooh!!!" there is a wide shot of the Dark Forest and the car at the top of the screen just as it starts to jump over the tree roots. In this wide shot at the bottom of the screen, the heads of two crew members are visible.
(at around 8 mins) In Harry Potter and the Sorcerer's Stone, #4 Privet Drive is a detached home. Only a garage connects it to the other similar homes on one side. A double car-garage home of a different design that is not attached to the Dursley's house (save for a fence that leads to the garden) stands on the other side. In this film, when Uncle Vernon is putting the bars on Harry's window, the house is clearly connected on both sides by two like homes, and there is no sign of the double car-garage house from the first film.
(at around 2h 15 mins) When Harry uses the basilisk fang to stab the diary, the ink from the diary appears to run across the uneven floor toward the water and up over a slightly higher stone floor panel. The ink should have pooled at the edge of the higher stone and run around either end of it.
(at around 1 min) When Harry tells Hedwig he cannot let her out due to being unable to perform magic outside of school, a key can be seen in the lock of Hedwig's cage, so Harry could've let her out at any time.
(at around 20 mins) The scene in Flourish & Blotts, where Hermione's parents are seen inside Diagon Alley, has been called a plot hole. Normally, Muggles cannot enter, or see, Diagon Alley. However, the Grangers are accompanied by Hermione, who, as a witch, would know how to enter through the Leaky Cauldron (and be able to see the pub). In the book, the Grangers comment to Mr. Weasley about having visited Gringotts to exchange their Muggle money for Wizarding money. If this is the case, they obviously aren't the first Muggles to enter Diagon Alley (indeed there have been numerous children who must have been taken there by their parents alongside a school staff member to buy their first year equipment for Hogwarts).
(at around 1h 4 mins) For most of the movie, it is shown that Moaning Myrtle is not solid, and that solid objects pass through her. However, when she jumps into the toilet, the water splashes. A splash can only be made by a solid object having sudden impact with water (this was also in the book). However, traditional ghost lore has ghosts able to move physical objects when they (the ghosts) are in an aggravated state of emotion, so we can assume the book/film follows that notion.
(at around 12 mins) When Harry first arrives at the Weasley's house, and Ginny first sees him, she's "star struck" at seeing him. However, she had already met him before he left for his first year. Of course, she didn't know who he was then, nor did the whole Weasley family, as Ron was also star-struck when he first met Harry on the train. Ginny wasn't at Hogwarts that year (so she couldn't have overheard it on the train or at the school), so she probably didn't know what Harry Potter looked like and she thought he was just another student at the station.
(at around 32 mins) The students are able to carry on conversations and hear instructions while wearing the earmuffs that protect them from the screams of the mandrake roots. We assume the earmuffs to be enchanted to specifically block mandrake screams, but not other sounds. Despite what "it says in the book" there is nothing in the movie to suggest that this could not be the case.
(at around 11 mins) The magic clock in the Weasley home shows a "Dentist" label. The series' running gag is that the Wizarding world has no idea what dentists are and what they do. However, this label was added by Arthur Weasley, a Muggle Studies anthropologist who could easily have learned about dentists through his studies.
(at around 1h 28 mins) When Tom introduces himself in the diary, his last name appears misspelled as "Ridolle" instead of "Riddle". However, as the name forms, what appears to be "ol" fleshes out together into the second D in his name.
(at around 1h 35 mins) McGonagall's new rules include "all students must be accompanied by a teacher to a lesson". However, it is later shown that there are only 9 teachers (including Dumbledore, Hagrid, the nurse and Filch). With 280 students in the school, this rule is impossible.
(at around 49 mins) In both the book and the movie, it is stated that Hogwarts was found over a thousand years ago. How can the entrance to the Chamber of secrets be located in a bathroom? There wasn't any plumbing a thousand years ago.
(at around 1 min) When Harry is flipping through his photo album at the very beginning of the movie, he views a picture of himself, Ron, and Hermione that should've been taken during the last school year, however, it's clearly a recent photograph as Ron and Harry both sport longer hair, and Hermione's hair is curlier.
(at around 48 mins) At the beginning of the transfiguration lesson, the writing on the blackboard behind Professor McGonagall is reversed, and this has been reported as a flipped shot. Further observation reveals that the right-hand board is, for undisclosed wizardly reasons, a mirror image of the left-hand board and so this might not seem to be an error. However, near the end of the scene, when Hermione asks what's in the Chamber, as McGonagall is answering 'The Chamber is said to be home...', she's in front of the right-side board and we get a better look. Although the drawing is indeed a mirror image of the left board, the writing is still flipped (we can see the words Lesson VI in front of the drawn peacock's beak as being backwards)
(at around 19 mins) In Flourish and Blotts, when Lockhart says "Which, incidentally, is currently celebrating its 27th week atop the Daily Prophet bestseller list!", the overhead camera pans up. As the camera passes his feet, Tom Felton's (Draco Malfoy) mark, two long strips of white tape are perfectly visible on the balcony floor where he stands.
As Harry is being chased by the basilisk down the tunnel, when it strikes at him just before he goes down a side tunnel the first time, you can see the bottom of the CGI basilisk head disappear as it comes into contact with the floor.
(at around 11 mins) When Ron, the twins, and Harry enter the Weasley home toward the beginning of the movie, there is a pan washing itself in the sink. You can see the edge of the circular cut-out in the pan used to make the brush spin in a circle.
(at around 2h 10 mins) Harry hides in the alcove with the basilisk in pursuit. The now blind basilisk stops and tries to sense if he is there and puts its head in to the alcove carefully avoiding the walls. Again after Harry tosses the stone to distract it the Basilisk carefully removes its head before moving on. These are not the actions of a blind animal.
(at around 52 mins) When Hermione presents her plan of using Polyjuice Potion to Harry and Ron, as the camera shows the page in the book Hermione is reading from the description redundantly reads 'Polyjuice Potion allows the drinker to transform himself temporarily into the physical form of an another.'
The goof items below may give away important plot points.
(at around 1h 50 mins) When Harry is reading off the paper that explains the Basilisk, he says "Spiders flee before it", but his mouth is saying something else. What Harry is actually saying is "and the crowing of a rooster can kill it." A scene was filmed, but cut in the theatrical version that shows Harry running into Hagrid, who is carrying a dead rooster and explaining that it's the second one he's found dead. The scene was later added on the second disc of the DVD as part of the deleted scenes section. The full text of what Harry is saying is "Spiders flee before it, and the crowing of a rooster can kill it."
(at around 2h 20 mins) Dumbledore asks, "Why then did the Sorting Hat place you in Gryffindor?" and in this close-up the Sorting Hat sits on two books. In the next shot, as Harry answers, "Because I asked it to." The hat now sits on three books in this close-up. During this entire scene in Dumbledore's study, things including the Sorting Hat and lamp behind Dumbledore to his right, change position depending on camera angle.
(at around 2h 25 mins) At the end of the year feast, when Ron, Harry and Hermione look up at Dumbledore after Hagrid has explained that Errol got lost delivering his release papers to Azkaban, you can see Katie Bell and Oliver Wood change position to keep watching Hagrid as he walks past them. In the next shot, Hagrid has not yet passed them, and they change their positions again.
(at around 2h 10 mins) When Harry is stabbing the basilisk in the mouth with the sword, he's supposed to have been stabbed by a fang at that moment. But if you look at his arm during the closeup, his arm isn't near any of the fangs, but when he pulls away he clearly pulls out a fang from on top of his arm.
(at around 2h) It takes Gilderoy Lockhart 6 seconds to fall down the entry to the Chamber of Secrets, but it takes Harry and Ron three times as long. In addition, when Harry and Ron land in the bone-covered room, crunching noises are heard from their landing on the bones. When Gilderoy landed in the room ahead of them, the crunching noises are missing (though they may have been too faint to hear over a distance in the tunnel).
(at around 2h) When Harry goes through the large round door and enters the Chamber of Secrets, he is carrying his wand in his left hand. When he sees Ginny on the ground and runs to her side, he clearly drops his wand from his right hand.
In the scene where Ron and Harry enter the flooding bathroom, all the sinks are overflowing. When they return later with Professor Lockhart, the faucet to the sink that they use to enter the chamber does not work, presumably because it is not connected (as in the following sequence).
(at around 1h 55 mins) When the Chamber finally opens, we first see Harry, Ron and Professor Lockhart from the front, and Harry and Ron are slightly behind Lockhart, and in a position to threaten and guard him. When you next see them a moment later from behind, Lockhart is behind them and they are in no position to guard him.
(at around 2h 10 mins) In the Chamber, when Harry runs from the Basilisk he ends up at a gated dead end, with steel bars that are embedded in a circular stone wall. When Harry crouches down, as the Basilisk's face nears, the manner in which the bars are embedded in the stone is actually quite different.
(at around 2h 15 mins) There is a scene where Harry is talking to Ginny in the Chamber, and he is holding his arm right below the wound. In this shot Harry has blood on his hand. When Ginny notices the wound, Harry moves his hand up to cover the wound. Now his hand is spotless. In the very next shot, however, Harry has blood on his hand again.
Just after Harry and Ron realize the basilisk is getting around by using the pipes, they walk fast down a corridor to warn people. Wires from a camera or a boom microphone are visible on the left-hand side of the screen.
(at around 2h 10 mins) After Harry climbs up the side of Salazar Slytherin's stone head in the Chamber of Secrets, the first time the Basilisk slams his face into the stone in the wide shot, the bottom of a crew member's denim pant leg and shoe are visible lying on a work surface, beneath the stone head's beard.
(at around 2h) Upon entering the Chamber of Secrets, Harry spots Ginny and runs towards her. After the last close-up of Harry's face as he runs, there is shot that faces Ginny, showing Harry's back. At the very start of this shot, on the bottom left corner of the screen two overhead studio lights, other equipment and scaffolding are perfectly visible, reflected in the puddle to Harry's left. Later when he runs out of the pipe, towards Ginny, some light reflections are visible as well.
(at around 1h 50 mins) Ron and Harry discuss the Basilisk's victims and, speaking about Mrs. Norris, Harry says, "There was water on the floor that night. She only saw the Basilisk's reflection." Just before Harry reads aloud from the paper again, the crew's gas torch canister with regulator and tip, that sits in a bucket beside another bucket, leans against the wall.
(at around 2h 20 mins) While Harry is in Dumbledore's study, in the two semi-overhead shots as Lucius Malfoy says, "So it's true. You have returned," and later when he says, "Come Dobby, we're leaving," sitting on the floor directly behind Dumbledore is a large steel piece of the crew's equipment, plus in the second shot another piece of equipment actually moves in front of the steel piece.
(at around 1h 11 mins) When Harry is in the library after everyone found out he is a Parselmouth, people are looking at him funny. One of the people they show is Ginny. Not long after that, Harry hears the basilisk and follows the voice up to a petrified Justin and Sir Nicholas. Since Ginny, while under the power of Tom Riddle, was the one who controlled the Basilisk, she could not have been calmly in the library at the time. She would have had to be out in Moaning Myrtle's bathroom controlling the basilisk.
(at around 1h 55 mins) When Ron and Harry run into Professor Lockhart's office, after they've just found out that Ginny has been taken into the Chamber of Secrets, Lockhart can be seen briefly in a mirror beside the door, waiting for his cue.
(at around 2h 20 mins) Near the end, when Lucius Malfoy is fuming at Dumbledore in his office, Malfoy's hair is fanned back behind his shoulders. The lighting in the room illuminates the back of his neck, where you can see Jason Isaacs' real, short brown hair.
(at around 1h 55 mins) Near the end of the film, when Harry and Ron find out that Lockhart's a fake, they push him towards the stone washstand in the girls' bathroom. When Lockhart touches the stand, it shakes considerably, proving that it isn't stone.
(at around 2h 10 mins) In the basilisk scene when you see a close up of Harry impaling the basilisk's head with the sword. The blood on the blade was obviously painted on beforehand as the bottom half of the blade has no blood on it.