Plot hole: The assassin cuts a hole in the glass to kill the Federation president. But with the size of the hole and the placement of the scope on the phaser rifle, the assassin would not have been able to see out of the hole.
Plot hole: Spoiler Warning. It turns out that Dan Merrick is actually Jack Stanton after a whole lot of reconstructive surgery to make him look like Dan Merrick. Everything is believable except that he has Dan Merrick's voice as well. He should have Jack Stanton's voice.
Plot hole: When the police chief asks Joe 'where's the briefcase they were telling me about?' Joe tells him to look in the back seat of the white BMW. There are a couple of problems with this. First, the police chief is looking for a case with a bomb in it, because he received a phone call from the guy who had his BMW stolen. Even if he knew about the money, which is unlikely, the police chief has no way of knowing that the case he is about to open is not a bomb, since no-one saw Marcone steal the case with the bomb in it. Yet he opens it without calling the bomb squad. Second, Joe saw Jimmy put the case with the bomb in the back seat, so why doesn't he warn the police chief about it? (01:35:00)
Plot hole: The pipe bomb that Maggie uses to kill Freddy is the same one that was found in Spencer's room earlier in the film. It's already been established that Freddy was erasing the people he's been killing from existence, so that pipe bomb wouldn't be there to use on Freddy.