Continuity mistake: At the bus stop when Donnie says to his sister that he'll throw her doll in the garbage disposal, watch the red-headed girl next to her. The girl positions her head differently each shot. From the front, she's looking at Donnie, and behind she's looking at his sister.
Continuity mistake: In the scene near the beginning in which Donnie's dad is using the leaf blower, the trees are covered with very green leaves while the ground is covered in very colorful ones. There are no naked trees anywhere or trees with leaves that have changed, and, when considering the amount of leaves on the ground, there should be many.
Continuity mistake: In the scene where the students are asked to write "They made me do it" on the blackboard, Sam Bylan is called up just before Donnie, yet on the principal's checklist Cherita is before Donnie and after Sam. (Despite any deleted shots, this is still a mistake in the theatrical release.)
Continuity mistake: In the scene where Donnie Darko and his sister are having a Halloween party, Donnie takes his girlfriend Gretchen upstairs while the song 'Love Will Tear Us Apart' by Joy Division is played. Watch closely as they ascend the stairs and keep an ear on the song as well. Somehow they manage to get all the way from the top of the stairs, to being sat down comfortably on a bed in someone's bedroom (with the door closed) without the audience hearing any interruption or 'jump' in the song whatsoever. This means they must have traversed the landing, entered the room and got properly sat down on the bed together in precisely no time at all. Quite a fitting mistake considering the movie's time travel theme.