Deliberate mistake: In the shot near the end of the film where Donnie grabs the keys for the station wagon, you can see a Blockbuster Video member card in a cup. That card design wasn't used until the mid to late 1990's. This movie is set in 1988. Deliberate as it's a product placement, but still wrong.
Deliberate mistake: During the "Sparke Motion" dance scene, the dance instructor is mouthing the wrong words to the song the girls are dancing to. "West End Girls" by the Pet Shop Boys was originally going to be the dance number, and that is actually the song playing for the recording of the scene. Richard Kelly couldn't get permission to use it, and "Notorious" by Duran Duran was substituted. The teacher is plainly mouthing words from the wrong song.
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.)
Audio problem: In the first dinner scene, look closely at the way Eddie Darko's mouth moves as he laughs after the "What's a f***ass?" question from Samantha. He takes a bite of his pizza, and his mouth movements do not match the sound of his laughter.
Revealing mistake: When Gretchen gets run over, you can tell that a dummy was used as the car's wheels pass over her. The position of her head changes between shots and her body seems a little too still for a living person who's just been run over. She should have been tossed a few feet or maybe even gotten caught under the car's wheels.
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.
Factual error: When Donnie returns to his house to find a jet engine has landed on it, we see them lift the jet engine up with the crane. Yet his family, complete with 5 year old girl, are standing right in front of the crane. Plus workmen are milling around underneath and about 4 FAA officials come from inside the house. They are lifting a 2000lb jet engine, and all these people are allowed to wander around while it's 20ft above them?
Factual error: In Donnie’s front lawn of his home which is supposedly Middlesex, Virginia, there are two very noticeable Sago Palms. Sago Palms are subtropical plants that grow nowhere near Middlesex. This is a direct clue to the filming location of Southern California...and not Virginia, which receives some snowfall on an annual basis.