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)
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)
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 Malfoy and his friends bother Ron and Hermione, Harry shows up and messes with the three boys. He grabs hold of Malfoy's feet, lifts them in the air and pulls him across the snow. In the first close-up of the soles of Malfoy's boots, not a speck of snow is on them, though he was just walking in it. Then in the next close-up, his feet still in the air, the soles are now covered in snow. (01:02:45)
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.