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: Mike already knows that Joe is back in town from Vegas because he spoke to him at his office after initially saying he was going to leave a message. He didn't inform Joe's wife because she asks him when he comes home. And Mike was at Joe's house when they talked because he has on the same robe when he steps out the closet from hiding. Why wouldn't he have already left if he knew Joe was back in town?
Suggested correction: Mike didn't think Joe was going to come home, especially if Joe was back in town but at his office. Plus, Joe told Mike he'd meet him at Mike's office in an hour. So, Mike took a shower to get ready. Making a bad decision, when you're in the middle of the poor decision to sleep with your friend's wife, isn't a plot hole.
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.