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.)
Plot hole: Monk steals the magazine from Coffey's SIG. However, I don't see how he could have jacked the slide to eject the round in the chamber without being noticed. Someone as paranoid as Coffey was at this point would not have left the chamber empty. (Just FYI, when you load an automatic pistol with a magazine, you have to pull back and release the slide to load the first bullet in the barrel.)
Add timeGrumpy Scot
Plot hole: Coffey uses the submersible "Big Geek" to carry the armed nuclear bomb to the NTIs. If Coffey was that desperate to blow up the aliens, he could have much more easily set the timer for 30 minutes, driven one of the submersibles far out over the abyss past the drop-off, and simply dropped the bomb down and let it sink under it's own weight.