Continuity mistake: There are two scenes during which Harry is shown having visions of the Dept of Mysteries while he is asleep. The first scene occurs after Harry's confrontation with Seamus in the Gryffindor common room. There are shots of Harry lying in bed wearing a short sleeve, crew neck tee shirt, but when he is startled awake by the vision of Voldemort, he sits up wearing a buttoned henley tee. The next day is the first day of Defence Against the Dark Arts class with Umbridge. That last shot of Harry in the henley tee shirt was cut from a later scene. Later in the film, when Harry has the vision of Arthur Weasley's attack, he is wearing the henley tee shirt. (00:34:00 - 01:09:35)
Revealing mistake: At the beginning of the scene near the end of the movie with Lucius Malfoy 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 his real, short brown hair. (02:22:05)
Other mistake: When Arthur takes Harry aside at the Leaky Cauldron, the moment before Arthur says, "There are some within the Ministry who would strongly discourage me from divulging what I'm about to reveal..." we can see the digital number "300" flash on the stone pillar to the right of the wanted poster. (This occurs only in the fullscreen version, as opposed to a widescreen version where the number "301" flashes underneath the poster, which is noted in another mistake). (00:17:30)
Continuity mistake: Straight after the second task Hermione wraps her own white towel round Harry, but between shots it jumps back to her shoulders, then back to Harry's several times. (01:35:05)
Visible crew/equipment: During the Quidditch match Harry's broomstick tries to shake him off, due to the spell. After Hermione tells Ron, "Leave it to me," in Harry's last close-up before he flips over, the seat that is attached to the broomstick, to make it more comfortable for Dan Radcliffe to sit on, is entirely visible. Glimpses of other seats can be had during the match as well. (01:20:50)
Continuity mistake: When Xenophilius draws the Deathly Hallows symbol, he draws it so that the bottom of the line touches the bottom of the circle. The shot cuts away and back again when he draws the triangle, but the line is no longer touching the bottom of the circle. (01:49:40)
Continuity mistake: In the dormitory, when lovestruck Ron is going gaga over Romilda, he is wearing a brown sleeveless tee shirt and its tan trim has many holes. When Harry brings Ron to Slughorn, Ron is still wearing that tee shirt, but now some of the holes are gone and the rest of the holes have changed position. (01:26:50)
Plot hole: One of Snape's memories show Lily telling baby Harry to be safe, be strong. That had to have occurred before Voldemort killed Lily. Snape was not in the house until after Lily was killed and Voldemort was gone. Only Lily and Harry should have had that memory, but not Snape.
Factual error: A theater marquee is visible promoting the showing of a film called Tribeca Follies. The acronym "Tribeca" - an amalgamation of "Triangle Below Canal [Street]" - didn't come into usage until the 1970s.