Plot hole: Immediately after the confrontation between Harry/McGonagall and Snape in the Great Hall, Harry runs up to Ravenclaw tower against crowds of students running the opposite direction. However, all the students would have been in the Great Hall during that confrontation, and therefore would have been coming from the same direction as Harry.
Other mistake: In both the books and the movies, Harry's Invisibility Cloak can always be seen until it is worn. In Diagon Alley, just before the Gringott's break-in, Ron pulls out the cloak to cover Harry and Griphook, but it turns invisible before he puts it on them. Ron merely mimes the motion of covering them.
Continuity mistake: Just after Harry and Lord Voldemort have their altercation in the Forbidden Forest, Neville is seen walking into Hogwarts' courtyard entrance to pick up the sorting hat. In the first shot, there is a camera angle of him from the waist down from behind, and he is stepping over the rubble and having no trouble walking. In the very next shot, you get a full frontal view of him walking, and he is limping and can barely move.
Continuity mistake: Throughout all the movies, the characters discuss several times how much Harry's eyes resemble his mother's. When we see flashbacks of Lily in this movie she has dark brown eyes. In past movies, when she was portrayed as a Hogwarts student, (in most of the same memories) she had blue eyes.