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: The military is content to acknowledge a missing B2 because a few people may notice one took off from a base and didn't come back (maybe it was transferred to a different base?). But after the detonation in the mine, they decide to cover it up as an earthquake. Seismologists all over the world can easily tell the difference between a nuclear detonation and an earthquake. The whole world would know that the US has set off a nuke and is lying about it, trying to claim it was an earthquake.
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.
Other mistake: The nuclear missiles are next to each other in the plane. But on the screen in the cockpit there is an empty spot between them.
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.
Factual error: In the scene when Travolta ejects from the Stealth, they are flying at 400 feet and 800 miles an hour. At that speed without a helmet or face protection, Travolta's face would be mush.
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.