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: Water pressure seems to be very picky in this film. It crushes Little Geek after passing 17,000 feet but somehow manages to leave Big Geek intact. Also if Big Geek could fall that amount of distance before imploding then why did Flatbed implode after only falling a few feet?
Plot hole: Why wasn't the umbilical to the "Explorer" unhooked from the rig after the rig was set down? Everyone knew things were going to get rough with the hurricane coming, so the umbilical should have been taken care of before the hurricane became a factor.
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.