Revealing mistake: During the car chase, when the first FBI car flips over, the device used to flip it over is visible on its underside. (00:45:55)
Continuity mistake: As Mason escapes from the hotel, we see him running down the escalators to the kitchen. On his way down, he pushed over two waiters who fall, the waiter on our left falls onto his back on the close up shot, but as the shot changes to the wide shot we see him falling again onto his front.
Plot hole: When Cage is hiding the VX gas balls at the end by putting them in a drain you can see he is holding the loose ball, but then in an instant cut picks it up along with the chip.
Continuity mistake: In addition to the incorrect time for the opening sequence in the chamber, in the initial close-up shot of Cage you can see a clock on the right. The two hands are both near the seven, so about twenty-to seven then. In the wideshot of him, the clock shows the time as quarter-to instead. The original twenty-to time is used for the rest of the scene.
Factual error: In the scene where Frye and Darrow confront Hummel after he sent the rocket off-course, Major Baxter barks at Darrow: "You're talking to a general, soldier. Maintain discipline." We've been told that all the men are Marines, and that even though they are committing treason, they view themselves as Marines. No Marine, particularly a career officer, would address another Marine as "soldier."
Continuity mistake: When the Marines are at the Naval Weapons Depot, one of them drops the cylinder carrying the VX Poison Gas. They run out, and when the guy drops the canister (containing the cylinder of gas), the cylinder with the gas has disappeared.
Other mistake: When Nicolas Cage is chasing Sean Connery in the yellow Ferrari, someone already mentioned that the windshield breaks more than once and in the next shot it's in perfect condition again, well I say forget even that. When Cage drives onto the sidewalk and crashes into the meters, the windshield should have been completely destroyed, not cracked. And the same goes for the hood of the car, which is in perfect condition in the next shot.
Factual error: Navy SEALs are highly trained operatives with a wide variety of technical skills, including training on 'special' weapons of which VX is a part. At least two of the team members, if not all, would have training on these weapons and would know at a minimum how to render them safe. This would eliminate the need for Goodspeed to accompany the team, despite his FBI HRT training rotation during training at Quantico. In this light, the team would not allow Goodspeed to accompany the team as he does not have their training, nor knowledge of how they operate and thereby put the entire team at risk. Were the SEALs to need a specialist, the team leader would have selected and flown in a military member(s) with first hand, and hands on expertise in that exact weapon system and versed in military operations as opposed to a civilian, even an FBI agent.
Factual error: During the Humvee/Ferrari chase scene, Goodspeed slides to a stop in a 180 degree spin, and then the driver's airbag inflates. There was no impact that would've caused the inflators to get the signal to fire, they don't just inflate because the car spun out of control.
Continuity mistake: At the end, when Nicholas Cage is being shot at on the light house, he has the green vx in his hand. Then when he reaches for the chip, it's on the ground again.
Continuity mistake: As the Seal team are about to enter the shower room we see them using fibre-optics to scan the area prior to entry. As they move the fibre-optic round towards the sensor we see that the camera is level with the sensor. The view from the fibre-optic suggests they are above the sensor. The angle in which they where facing the sensor also changes.
Factual error: When Cage gets into the Ferrari, the camera changes for a few seconds showing the gearbox. In slow motion it is obvious that Cage shifts into 3rd gear instead of 1st, however the car makes a very impressive tyre-burning start. The F355 is indeed a very powerful car, but this would be simply impossible to do in 3rd gear. (00:44:14)
Continuity mistake: When Ed Harris decides to shake things up by firing one of his rockets, the FBI radar tracks the trajectory and determines that it is heading to Oakland. More specifically, the rocket is heading to the Oakland Coliseum where there is a football game being played. But when the movie shows the rocket as it is flying towards its target, the rocket flies over a hill and we see the packed stadium - Candlestick/3Com Park in San Francisco.
Continuity mistake: When Nicolas Cage drives through the window in the yellow Ferrari and the shot changes, he is coming out from a different window than in the first shot. In the first shot he emerges from the window to the left of the 7th Street Garage storefront ('Classic Autos' written on the window), but next shot he emerges from the window to the storefront's right. Also, note the now glassless window to the storefront's left, due to a previous take.