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.
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.
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.
Factual error: At the end there are F-18s that have United States Air Force painted on the side of them. There are not, nor have there ever been F-18s in the Air Force.
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.
Revealing mistake: During the big chase scene when the tram is out of control as it hits the last car and blows up you can see rubber tires on it, specially added to let it go on tarmac.
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."
Factual error: When the Seals team swim towards the rock they are aided by microsubs, which all have headlights that are on. The light would be reflected at the surface and would be detected in the blackness that is all around. They do not need lights, all they need is modern technology to direct the subs, which they have. Details like this would have been determined during the planning of this operation, and fully trained Navy SEALS would know better either way.