Plot hole: When Evan is in jail with the religious prisoner trying to get him to help him get his journals back he goes to the scene where he is drawing that homicidal picture in kindergarten, but he gets up and puts the spikes that holds documents through his hands, creating a stigmata-style scar. The religious guy in the cell with him is so amazed because of this he thinks Evan is a prophet and he decides to help him. If Evan had gone back in time and got those scars on his hands, he would have changed the original timeline and would have arrived in jail with those scars the whole time. Some people try to correct this using the "If I can create scars, then can I fix them?" statement Evan made to defend the mistake and suggest he can create instant scars but he was using the word "scars" to refer to the negative events; not literal scars on his body. The scar he got when he burned himself in the past didn’t magically appear on him the moment he returned from the past; it became part of a new, slightly altered timeline (just like the scars on his hands should have been) and it let him know he can change history.
Continuity mistake: After little Kayleigh picks up the blockbuster, older Evan is now at Sunnyvale Institution. The blankets are not tucked under the mattress, then they are tucked when he gets out of bed, and in the shot from under the bed, as he searches for his journals, the blankets hang down to the floor, yet in the next shot they are not.
Continuity mistake: After Evan beats Tommy to death on the college campus, it shows him kneeling over the body, and there is no blood on his collar. The shot changes to Kayleigh screaming, then back to Evan, in the same position, but now with blood splatter on his collar. He had already finished assaulting Tommy, so there shouldn't have been anymore blood spray.
Continuity mistake: When Ashton Kutcher convinces his jail bunkmate that he is personally in touch with Jesus, by using his journal to cause stigmata to appear on his hands, a stigmata mark can be seen in his right palm before he changes the past (just as he mumbles "tell me if you see anything weird").
Plot hole: In the scene where Evan is in Sunnyvale institute and demands his journals, the doctor says he has never had any. The very same doctor told him to start writing in journals when he was seven before he killed Kaylee, so when Evan went back in time to destroy the firework, he couldn't have erased journals that were written before that. Evan was only allowed to write 2 pages before the incident where he killed Kaylee. This event completely altered his history, allowing the courts to place him in the mental hospital afterwards. There was no continuation of writing the journals because in this timeline his blackouts were not the main issue.
Other mistake: When Evan finishes talking to the "prostitute Kayleigh" on the restaurant, he goes to his room, which finds his friend having sex with a girl. When Evan demands them to leave the room, he sits on the chair, and opens his diary, but you can see that when he opens it, the pages are empty. He doesn't turn to another page before he begins to read, so he appears to be reading from the blank page.
Plot hole: When the frat boy bursts into Evan and Kayleigh's romantic dinner to tell him his car's been trashed, he says he's been looking all over for Evan. But he was sitting right there watching the whole time Even was giving the pledges their instructions for helping him set up the romantic dinner (which necessarily included the exact time and place), so shouldn't he have known where Evan would be?