Plot hole: When the diesel train stops in the tunnel, one of the soldiers tells another one how far they are from the spot where the nuclear detonation will take place. Do the math: the distances don't work out. At least one of the trains would have to do over 100mph AVERAGE to put enough distance between them. Military precision, indeed.
Plot hole: When the two remaining American helicopters return from their incursion into Russian airspace, both land outside the operational HQ hangar. This is fine, except for the question of where the eight warheads that they recovered have gone to. Surely they would have brought them back to the base rather than just leave them on the bridge, but if they had, then shouldn't they either have them underneath one chopper when they both land? Or if the chopper carrying the warheads had offloaded somewhere else on the home airbase, why did both helicopters land at the same time outside the HQ hangar?
Plot hole: After Vlado was shot and his brother (the one with the bomb) was carrying him, there's no way Tom and Julia shouldn't have been able to catch him. He was MUCH slower carrying Vlado and they should have been able to catch up to them in no time. And there were other law enforcement following DeVoe. There was only one way out of that alley. Why weren't they at the entrance?