When Valerie tries to call the local sheriff by CB radio, she's interrupted after saying "This is Valerie Dwyer. We saw something on the road--." Yet a police report of the call seen later omits her name, which she gave, and includes the information she didn't get to: it says "FEMALE VOICE GIVING INFORMATION REGARDING LANDING OF UNIDENTIFIED AIRCRAFT."
Gordon tells Gaiter, at gunpoint, to change the serial number on his BDU in the computer to "AF-463908-SW," but we see on her screen a pop-up dialog showing it being changed from "AF25828-BDU" to "AF46398-BDU." Meanwhile, in the background window of her screen, highlighting and out-of-sequence serial numbers seem to show that "AF25828-BDU" and "AF46398-SW" have been interchanged.
Gaiter's screen shows that 4 Sidewinder and 2 Sparrow missiles are being ordered for Gordon's Mirage III, in addition to bombs. The Mirage III can't carry that many weapons, as it only has 5 hard points. Nevertheless, Gordon's onboard display has icons for 11 weapons. He actually fires more of them than that, but the display does not count down consistently. Also, when when we actually see Gordon's plane it always seems to be carrying just 2 Sidewinders, and every time we see him fire one, it's one on the left.
Glatman, the nuclear weapon expert, refers to dangerous "plutonium gas" inside the weapon. Plutonium is a solid; the only radioactive gas that might be in a nuclear weapon is tritium.
At about 48 minutes into the movie, a maroon Ford Aerostar is shown. Just a few moments later, the van has changed to a completely different Ford Aerostar, most noticeable by the different wheels.
At about 1:04 into the movie, Valerie is in the van, as she reaches for the gear lever, the shot is clearly of an entirely different vehicle.
Without Gaiter doing anything, the display then changes for no reason to display a labeled diagram of the type of weapon that "AF46398-SW" is.