Crew or equipment visible: When Donnie and his dad are talking in the car - just before they almost run grandma death over - a clapperboard is reflected in the window behind Donnie's Dad's head.
Incorrectly regarded as goofs: The unmarried Jim Cunningham wears a wedding band throughout the film. According to Richard Kelly, this is an element of his untrustworthy and mysterious nature.
Continuity: While in the car with his father, the passenger side mirror can be seen outside of the window. During the back and forth shots between Donnie and his father, the mirror noticeably changes angles.
Revealing mistakes: When Donnie finds the .45 pistol in the closet the hammer is not cocked and the safety is on. It is impossible to engage the safety on a .45 unless the hammer is cocked. And there is a screw or pin visible in the rear left side of the slide which does not exist in a real .45.
Continuity: During the Life Line activity in Mrs. Farmer's class, the Asian girl Cherita answers her question card by placing an "X" on the chalkboard. When Donnie is called next the "X" that Cherita placed on the board is barely visible, like it had been half-erased.
Incorrectly regarded as goofs: The movie is set in 1988, but license plates, book editions, news photographs and products from 1989-1999 appear throughout. These anachronisms fit in with the movie's themes of time travel and altered realities. (Chapter 4 even mentions how things from the future, such as Mayans having arrow heads, are symbols of future being brought to the past - these anachronisms are on purpose.)
Incorrectly regarded as goofs: When the students all write "They made me do it" on the board, Sam Bylen is followed by Donnie Darko. Cherita Chen wrote between those two, but the original cut skips her moment. It is restored in the director's cut.