Continuity mistake: In the scene right after Evan visits Lenny for the first time after 7 years, he is lying on his dorm bed, flipping through his old notebooks. The scene starts out with him biting the nails on his right hand, but in the next shot when the notebook starts shaking, both hands are visibly holding the notebook.
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.
Revealing mistake: In the first scene of the film, Evan is writing frantically in a journal and his last words that the camera zooms in on are "Save her". Look closely and you can see that those same words are already indented on the page as indicated by a visible letter "s" and "h" and a period that had already been written on the pad of paper. Obviously they had done some other takes. (00:01:35)
Continuity mistake: When Evan goes back in time to when they are putting the blockbuster in the mail box, his cigarette falls out of his mouth and onto his shirt. He gets burnt, as is shown when he returns to modern times, but all the rest of the scenes with them in the forest just after it happens, there is no burn mark on his shirt.
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.
Audio problem: When Kayleigh, Tommy, Evan and Lenny are putting the block buster in the mailbox, Evan puts the cigarette on the block buster and says it should last Lenny 2 minutes, but his mouth says 10 minutes.
Continuity mistake: When Evan takes Kayleigh (who is now a drugged up hooker) to a diner, there is a plate with a piece of pie, a wallet and a red cigarette lighter on the table in front of Kayleigh. Each time the camera turns to Evan and then back to Kayleigh, the lighter is in a different location. This happens several times.
Continuity mistake: When Evan has a nosebleed after finding out that he has no hands, there is blood on his neck that disappears and reappears between shots.
Visible crew/equipment: In the last scene, when Evan is walking down a busy Manhattan street, talking on the cellphone, you can see the red camera truck's reflection in a window on the other side of the sidewalk.
Continuity mistake: Young Evan puts the cigarette on the fuse of the blockbuster, and as Lenny walks away the butt is shorter than when Lenny stands up near the mailbox, after tying his shoe lace. (00:12:25)
Continuity mistake: When Evan and his mom came out from the psychic, she confessed to Evan that she had two stillbirths before Evan. But during the last scene, when baby Evan was trying to kill himself, we hear a different dialogue saying that his mom had three stillbirths before getting him. (00:42:26 - 01:52:09)
Continuity mistake: While Evan talks to the "prostitute Kayleigh", the piece of pie on the table changes position between the shots.
Continuity mistake: After Kayleigh's suicide, Evan travels back to time to the part when he's in Mr. Miller's basement. When young Tommy appears on the steps, he leaves a small opening on the door, but when Mr. Miller argues with him about keeping the door shut, you can see that the door is wide open, which it wasn't in the shot before.
Continuity mistake: In the original junkyard scene Kaylee is wearing a completely different outfit than later on when Lenny kills Tommy. The first scene she is wearing two shirts and some high waisted, ill fitted jeans. Then when Lenny kills Tommy she's wearing a bright blue with white stripes spaghetti strap shirt and tight, well fitted jeans. Plus, a lot of the points of time travel change throughout the movie. In the original junkyard scene they have already made it to Tommy and Kaylee has been hit by the board before Evan has his blackout. When Lenny kills Tommy they're still walking through the junkyard. It could be argued that it has to do with where he started reading from the journal but the blackouts from his childhood are predicated on his future trips into the past. So he should have blacked out before he ever made it to Tommy.
Suggested correction: It's safe to assume that the basement incident and probable continued abuse in the first timeline destroyed Kay-lee's self worth, image, and esteem. In a world where that never happened, she would definitely at least of been dressing differently (the point would have been better illustrated had her hair been different too). As for the second part, I'd have to agree, unless in Evan going back the first time he changed the day Tommy decided he wanted to kill Crockett, this changing the exact day of the blackout. And changing what Kaylee was wearing, I guess.
