Plot hole: They go and buy Anne Marie a whole new wardrobe. So, how come in the remainder of the movie she continues to wear her old rags?
Plot hole: We discover that Teresa the maid has been turned into some kind of living zombie at the end of the movie. She confronts Alex and Megan near the end, and they run away from her and then fight with the Puppet Master. The issue of Teresa is then never addressed in the rest of the film, she just simply disappears from the plot and the scene. (01:13:35)
Plot hole: Granted, Coffee is suffering from "high-pressure nervous syndrome," but if you're a Navy SEAL, wouldn't you notice whether or not your pistol has a magazine in it? Monk pulls the clip out of his jacket and starts knocking rounds out of it for the rig crew's benefit; the same dramatic effect could have been achieved with a handful of cartridges he could let slip through his fingers. You could argue that Monk didn't have enough time to unload the gun and replace the magazine, but in that case, I think the scene where Monk briefly had the gun should have been a bit longer. (Even had the empty magazine been IN the gun, Coffee still might notice the difference in weight, but that would be easier to suspend your disbelief for.) (01:43:53)
Plot hole: Megan is suspended because the police were not able to find the gun the robber had (stolen from Eugene at the scene) and believed that she had killed an unarmed man. This is very unrealistic because surely they would have interviewed all of the hostages/witnesses at the robbery and each would have easily confirmed that the robber had a gun, and possibly that Eugene might have been missing right after the incident.
Plot hole: After Ann retrieves Tibor Zoldan's music box from the pawn shop, she finds the incriminating photos of her Nazi father, Michael Laszlo, hidden in it. Even though Zoldan (who had died) could have redeemed the music box from the pawn shop within a certain time period, it makes no sense that he would have pawned it with the photos left inside. The photos were how Zoldan was able to blackmail Laszlo. It's highly unlikely he would have forgotten they were in there.