(at around 1h 28 mins) When Harry is in the prefect bathroom, solving clue two, we clearly see that the egg is still open as he pulls his head out of the water. Yet, in the very next shot, when his head is above water, we see the egg closed and no sound coming from it, as it is in all shots after that. He would not have been able to close it from one shot to the next.
(at around 1h 50 mins) When the contenders enter the third task arena and during this scene, there are mismatches between the bass-drum sound and the video of the girl playing it seen in the background of the scene.
(at around 1h 35 mins) In the scene following the second task (when Dumbledore is announcing the standings) you can see Neville with Karkaroff behind him. Karkaroff has his hand on Neville's shoulder. Not only is Karkaroff from a different school, but he is a Death Eater who knew that Neville's parents were aurors (he implicates their torturers in the Pensieve scene) and would not want to touch him as he would be viewed as a blood traitor.
(at around 42 mins) Harry's godfather Sirius Black is in hiding and using codenames in correspondence. Surprisingly, when he sends an owl post to Harry, he writes Sirius' real name on the envelope rather than a codename.
(at around 23 mins) When Alastor "Mad-Eye" Moody writes on the board, he incorrectly spells "unforgivable" as "unforgiveable". The letters surrounding the inserted letter are noticeably indistinct later on.
(at around 2h 15 mins) When discovered, Barty Crouch Jr. tells Dumbledore "Lord Voldemort is back". It is established in the Potter universe that Voldemort name is never spoken (an exception being Dumbledore and Harry), let alone by death-eaters, who do not dare to. Someone as Barty Crouch would have said "the Dark Lord".
(at around 18 mins) When the Beauxbatons students enter during the opening feast, Seamus is sitting behind Ron on the near side of the table. After Moody enters and "fixes" the ceiling, he is sitting next to Hermione and Ginny on the far side of the table.
In the scene showing the arrival of the Beauxbatons ladies, the
shot of Ron and Harry being overly-excited, Hermione and Ginny are sitting next to each other as they show a little bit of disgust at the boys' reaction to Fleur. In the next shot - after the Beauxbaton ladies move past Harry and Ron, they show Ginny and she is sitting next to another girl - not Hermione.
(at around 1h 35 mins) After Harry climbs out of the lake, Hermione covers him with a towel she was wearing moments before. The shot changes to an overhead shot, and Hermione is wearing the towel again. In the next shot, she is putting it on Harry again.
(at around 1h 35 mins) At the end of the second task when Seamus tells Dean to get Harry another towel, he is putting a towel around Harry's neck. In the very next shot the towel is draped over Harry's shoulders and back.
(at around 1h 19 mins) When the band is playing the fast song at the Yule Ball, Crabbe jumps with his hands on Victor Krum. When the camera zooms in on Krum and Hermione, Crabbe is not standing near Krum.
(at around 57 mins) In the tent where the champions are preparing for the first task, Karkaroff and Krum look around and stand up slowly when the cannon is fired. In the very next shot, they are standing up and away from the center of the shot.
(at around 59 mins) After the Dragon crashes through the teachers stand during the first task, Snape can be seen helping McGonagall to her feet but in the next shot, they are both on the floor and are only just trying to get up.
(at around 45 mins) When Harry is talking to Sirius through the fire, Ron stumbles in on them talking and says that he heard voices. Harry quickly dismisses this and Ron leaves. The camera then goes to a wide angle shot of the room where you can see Ron walking in an upstairs balcony. From this position, Ron would have clearly been able to see Harry talking into the fire with Sirius, and would have never have had to come down stairs and ask about the voices.
(at around 51 mins) When Moody chases Malfoy around the tree after he is transformed back from a ferret, he sticks his walking stick in the ground and it is tilted. In the next shot, you can see the stick in the background and it is perfectly erect.
(at around 1h 11 mins) When Fred asks Ron who he is going with to the dance, when you see the letter being passed to Ron, it has four lines of writing at the top of the page, but when Ron reads it, it has only three lines in the center of the page. You can also tell that the writing is very different in both shots.
(at around 1h 8 mins) When Ron makes fun of Eloise Midgen, the close up shot of Midgen shows a white girl on her right, then a black girl. On the full room shot, the white girl vanishes from sight, and the black girl is next to Eloise Midgen.
(at around 1h 40 mins) After Harry falls into Dumbledore's Pensieve, he sits next to him and says "Professor?" Behind him you see two women approach and sit down. The camera angle changes to show someone stick his hand through Harry and shake Dumbledore's hand. You can see the same two women approach again and sit down again.
(at around 16 mins) When Headmaster Dumbledore is announcing the arrival of the Beauxbatons and Durmstrang academies, Filch is seen running towards Dumbledore to warn him of the arrivals. In one scene it shows that Filch has run at least 20 feet past Ron and Harry. In the next scene the camera pulls to a closer shot in which it shows Harry and Ron are startled to see Filch *just* run past.
(at around 1h 3 mins) After the first task, when Harry opens the egg for the first time, he can use both his arms easily. In the next scenes (breakfast and dance lesson) he has his left arm in a sling.
(at around 1h 28 mins) When he has emerged from the bath water after listening to the egg, Harry is sitting with Myrtle and his hair changes repeatedly between shots, going from completely smooth to having a bit of hair sticking straight out on his right side.
During the first lesson Hermione moves between two seats. To start there is one person between her and Seamus, and she isn't at the front, she then moves to the front row and there are two people between her and Seamus, then she moves back to her original seat.
(at around 2h 5 mins) In the wand connection scene between Harry and Voldemort, Harry raises his left arm to steady his wand. The camera angle switches, and his left arm is still beside him and then he raises his arm again.
(at around 10 mins) As Ron is talking about Viktor Krum one of the Weasley twins takes off the Irish flag he's wearing and throws it over Ron's shoulders, Ron is seen taking it off in one shot and when Ginny makes her comment he's seen removing it a second time.
(at around 1h 1 min) When Harry is being followed across the roof by the dragon, he falls and the close shot shows his broom stuck to the roof of the dormer he is on. However when the shot is seen from the dragons POV the broom is not there. When they return to Harry the broom is now on the roof again.
(at around 2h) In the graveyard, after Wormtail puts the bone in the cauldron, he places Voldemort's wand in the left inside pocket of his coat. Later, when Voldemort asks Wormtail for his wand, Wormtail pulls it out of the right inside pocket of his coat.
(at around 31 mins) When the names are drawn from the Goblet, one of the Weasley twins appears to be two places at once. When Harry sits down on the risers, there is a Weasley twin sitting down farther on the row. In a long shot, both Weasley twins are sitting together at a table on the other side of the hall.
(at around 1h 45 mins) When Professor Snape confronts Harry in his Potions Store, and accuses him of stealing supplies, the portraits on the walls behind them do not move and are completely stationary. All magical portraits, paintings and photographs move, even when asleep.
When Ron and Hermione are shown under the lake during the second task, they're wearing their uniform robes. They were not, however, wearing them the previous night when they went to Prof. McGonagall's office and were taken for the task.
During the arrival of the Durmstrang students, each of them is carrying a staff. The lead student in the procession puts his staff on the ground before running up the aisle. After performing a short dance (without his staff), we see him blowing fire from his wand. The staff reappears in his right hand, and his wand is in his left. In the next shot, the wand is in his right hand and the staff is gone.
(at around 2 mins) At the beginning of the film, when the caretaker is walking to the big house, the flashlight (torch) is in his left hand. When he gets to the outside steps, he switches it from his right to his left hand.
(at around 1h 45 mins) When Harry has just seen the memory of the court, and gets back to the "real", Dumbledore is standing next to the Pensieve. He's standing up straight, and when Harry walks towards the Pensieve to look into it, he's not looking at Harry. However, in the next shot (in which Dumbledore's sentence starts with: "You see, Harry..."), Dumbledore leans towards Harry. Also, he's holding his wand in his right hand.
(at around 25 mins) When Alastor Moody uses the Imperius curse on the spider, he moves it from his right to his left, from Parvati's shoulder to Ron's head, but in the next shot, the spider is moving from Moody's left to his right, as if the spider is coming from the left side of the classroom, and not the right.
(at around 2h) When Lord Voldemort summons his Death Eaters and tells them that he was disappointed, we can see that he reveals the mask of each and every character. The fourth character however is not wearing a mask, he can be seen standing whereas in the next shot he is sitting.
(at around 2h 10 mins) When Harry is in Moody's office after the third task, and Moody closes the cabinet door after searching for more potion, a crew member in a white shirt is reflected in the cabinet's glass.
(at around 28 mins) As Harry, Ron and Hermione are leaving Professor Moody's first class, a female extra can clearly be heard saying "I have Professor Lupin next", which is impossible as Lupin is no longer a teacher and left Hogwarts at the end of Harry Potter and the Prisoner of Azkaban.
(at around 42 mins) In the note Sirius sends Harry, he asks him to meet him in the Gryffindor common room at 1 o'clock on Saturday night, there is no such thing. He should have said either 1 o'clock Saturday morning or 1 o'clock Sunday morning.
(at around 18 mins) Dumbledore introduces the Bulgarian Sons of Durmstrang "from the North." Bulgaria is far south of England, just above Greece and Turkey, but Durmstrang School is not in Bulgaria. It is in the Arctic Circle, with a diverse clientèle including Bulgarians and Germans.
At the end of Harry Potter and the Prisoner of Azkaban when Harry gets his Firebolt it is black, but in this film his Firebolt is gold and maroon with handles on them. Considering Gryffindor's colors are gold and maroon, and Harry is on their Quidditch team, it only makes sense that he'd modify it for better performance and appearance in Quidditch matches.
During the Quidditch world cup camp scene, you can see what looks like a Niger flag instead of an Irish one. The two are similar, but the Irish flag has vertical green, white and orange stripes while Niger has horizontal orange, white and green stripes with an emblem. However, at a world cup it is only natural that there are people from several nations, not just the two competing in the final. We can also see an American, a Romanian and a Ugandan flag, amongst others, in that particular scene.
(at around 1h 3 mins) When Harry opens up the Golden Egg in the Gryffindor common room, you can clearly see the Patil twins in the crowd. However, in the book, Padma Patil is not in Gryffindor, she's in Ravenclaw. As stated in the trivia section, they changed Padma to being in Gryffindor instead of Ravenclaw. The twins are shown multiple times in the movie as going places together, and saying things in unison.
(at around 1h 55 mins) When in the maze, Cedric uses the spell "Expelliarmus" on Victor Krum causing him to fall unconscious, when "Stupefy" is the usual charm one would use for that. However, these spells are similar enough to confuse devout Potter fans, and this scene is accurate to the book.
(at around 19 mins) In the great hall when Hagrid stabs the choir director with the fork you can clearly see that his eyes look over the choir director's head, this is because of scaling issues Robbie Coltrane's reaction as Hagrid had to be filmed on a blue screen and then later added into the frame. Robbie Coltrane was probably looking at a misplaced marker.
(at around 21 mins) When Barty Crouch Sr. is explaining the rules of entering the Tournament and Dumbledore is subsequently yelling for silence, there are a few shots where you can see that Alan Rickman's, Predrag Bjelac's and Frances de la Tour's stand-ins/doubles are being used.
(at around 16 mins) When watching the arrival of the Beauxbatons contingent (a stagecoach pulled by seven winged horses), the Hogwarts students are looking in different directions. Some are still looking at the sky, some looking down, others looking straight to the front/camera.
(at around 24 mins) When "Mad-Eye" Moody tells Finnegan to not put gum under the desk, he chucks the chalk at him but it bounces off the table behind him and into the girl sitting there before cutting away, suggesting the chalk was rubber.
(at around 1h 25 mins) In some scenes, there is no glass in Harry's glasses, such as the scene where Harry and Hermione are talking on the bridge. Near the end of the scene, there is clearly no glass in Harry's glasses.
(at around 29 mins) When Fred and George are attempting to put their names into the Goblet of Fire, they are talking to Hermione. One of the twins clearly tries to say his line early and is cut off by the other one continuing to talk.
At the start of the "Third Task" (the maze), Dumbledore (Michael Gambon) states that Cedric Diggory (Robert Pattinson) and Harry Potter (Daniel Radcliffe) would enter the maze together, since they were tied for the lead in the Triwizard Tournament; however, Harry enters alone.
When "Moody" (Brendan Gleeson) turns Draco Malfoy (Tom Felton) into a ferret, he sticks the animal down the front of Vincent Crabbe's (Jamie Waylett) pants; however, moments later, the ferret emerges from the leg of Gregory Goyle's (Josh Herdman) pants.
(at around 2h) Part of the incantation used to return Voldemort to power is "Bone of the father, unwillingly given". It would make more sense to be "unknowingly given," as it says in the book, as someone who is deceased cannot give something unwillingly or otherwise. (Interestingly, this goof is actually corrected in some of the dubbed versions, like Swedish and German, where the words in this part are directly lifted from the novel.)
In earlier movies (and future ones as well), whenever a character takes Polyjuice Potion, their voice does not change to sound like that person and they continue to sound like themselves. However, when Barty Crouch Jr. takes Polyjuice Potion to look like Mad-Eye Moody for almost a year, his voice always changes to sound like Moody's. It should be noted that in the books, your voice does change when you take Polyjuice Potion to sound like that person.
(at around 2h 10 mins) When Dumbledore is comforting Harry after he has returned from the graveyard, McGonagall can be seen putting her hand on Harry's shoulder, but the very next scene shows her standing far away, next to Snape, as Fudge tries to keep Cedric's death quiet.
(at around 2h 10 mins) During the post-cemetery sequence where the crowd is reacting to Cedric's death, Neville appears to be in two places at once. He is given a close-up reaction shot towards the end of the scene, and he is standing between two students. In the shot directly preceding this however, he can be seen on the far right edge of the screen; an unidentified female student is on his left, and she disappears from in the next shot (his close-up).
(at around 2h 5 mins) At the cemetery, when Harry is trapped at the statue, Voldemort raises his right arm and places his finger on Harry's head. While Voldemort's arm remains raised his sleeve slides down towards his shoulder, but is back up at his elbow in the close-up.
(at around 2h 15 mins) At the end of the movie in his address to the students, Dumbledore says that Cedric Diggory was murdered by Lord Voldemort. In fact, Wormtail was the one who killed Diggory at Voldemort's orders. Voldemort was still in such a form that he could not raise a wand. However, Dumbledore's words in the movie are an accurate repeat of those in the book. Dumbledore was speaking figuratively; a literalist would say that Diggory was killed at Lord Voldemort's command.
It has not been explained, how Neville got a gillyweed, which had to be stolen from Professor Snape's office. In the book, it was stolen and given to Harry by Dobby, but in the movie a whole thread of house-elves was omitted. False Moody did not claim to have given Neville the gillyweed itself, only a book on magical plants (in accordance with original book).
(at around 2h) For Voldemort's resurrection, Wormtail cuts off his hand at the wrist, but despite having severed some very important veins & arteries, there's no apparent hemorrhaging from the open cut as one would expect. He doesn't even seem to be in any considerable pain for the remainder of the scene, let alone passing out (or dying) from the inevitable blood loss. Besides, it seems extremely difficult to cut off a hand with a knife this way, even when the person is motivated to do so.