Plot hole: There is no logical reason as to why two pilots on a training exercise would be given classified info such as the access codes for the nukes.
Factual error: During the scene on the train when Hale arrives in the helicopter, Deakin and Kelly shelter themselves from the incoming fire by hiding behind the walls, and manage to avoid taking any hits. This is odd considering they're sheltering not only behind wood walls, but wooden slats. The M16 with its 5.56mm rounds would easily penetrate the wood, let alone pass through the gaps, and injure, if not kill, our lovely villains. Even if they magically escaped unharmed, there would be bullet holes visible inside the train carriage, but these do not exist when the camera pans through it. Indeed, later on the train, Kelly fires a shotgun which happily penetrates the sides of the carriage. There is no reason an M16 would not be able to.
Continuity mistake: Despite a nuclear explosion sufficient to cause the ground to ripple for several kilometers, strangely, it is not sufficient to blow the top of the mineshaft.
Continuity mistake: When Deakins drops the nuclear weapons out of the stealth, the parachutes on the nukes are white. When the recovery team finds the nukes, the parachutes are black.
Continuity mistake: After Travolta drops the nukes from the stealth, he says "This is Deakins! Hale's lost it! I'm punching out!" When the G-man on the plane asks for their last transmission to be faxed to him, the transcript says "This is Deakins! Hale has lost it! I have to punch out!" Important government documents, such as this, would have to be word for word, especially with an issue of missing nukes present.
Continuity mistake: When Slater throws the henchman out of the first Humvee, he lands on the side of the road. But then he is in the middle of the road so Travolta"s Humvee can run him over.
Continuity mistake: When Wilkins' helicopter blows up, the train comes to an almost complete stop and then goes through the tunnel slowly. When Hale and Terry are done sabotaging Deakins helicopter, the train is back to full speed.