Corrected entry: If you look at the top of the school building there is an abbreviation "LHS" which presumably stands for a high school's initials. But the school that Donnie attends is called "Middlesex Ridge School." (Filming location was at Loyola High School in Los Angeles.)
Corrected entry: There is no point to having the students give an in-person sample of their handwriting, because any one of them could alter their writing if they wanted to. It would make more sense to collect previous examples, like homework. And anyway, the original graffiti was made with spray paint and was in very large text, both of which would affect a person's handwriting style and make finding a match very difficult.
Corrected entry: In the scene where the principal is asking the students to come up and write "They made me do it" on the board, he calls Donnie up to write. After Donnie writes the phrase, the principal puts a check mark next to Donnie's name on the clipboard. If you look at the phrase on the ground and on the board, there is a distinct difference in how it was written, so Donnie should have been totally ruled out.
Corrected entry: When Donnie Darko returns to the cinema after throwing gasoline all over Jim Cunningham's room and setting it on fire, surely when Gretchen awakens she'd smell it on him? I also find it hard to believe she's slept through the soundtrack of a horror movie yet awakens at the sound of Donnie taking popcorn from her.
Corrected entry: When Donnie and Gretchen are on Carpathian Ridge talking about Grandma Death, Donnie appears to sit down on the green couch behind him. In the long shot of them both, he's sitting in a normal chair with a high back; even if he had sat down in the chair, the back still would have been visible.