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.
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.
Continuity mistake: When Goodspeed tries to call his girlfriend and tell her not to come to San Francisco, she tells him she is going and hangs up the phone on him. The phone and her are in front of a window with a skyline in the background. Goodspeed lived and worked in Washington DC, but the skyline in the window is that of Los Angeles. You can recognize LA's tallest building in the background, Library Tower.
Continuity mistake: After the shower scene, the bad marines are searching for Mason and Goodspeed. When the 2nd grenade explodes and the 2 are running away, Mason is in front but when the two dive into the water and the shot changes to from beneath the water Mason has somehow managed to get behind and on the other side of Goodspeed.
Continuity mistake: When Mason and Goodspeed make their way to the morgue, Mason disposes of a marine with his straight-as-an-arrow knife throw. Watch very carefully, as there is a split second during which the marine appears to sustain the impact of the knife, and we hear the sound of it. But there is no knife to be seen until the next shot, where he is gasping for breath and trying to pull the knife out of his neck.
Continuity mistake: When Goodspeed is on the roof of the lighthouse with the last pearl configuration of poison gas, one of the 'pearls' drops off the bottom. As he chases it across the roof, from the front shot he has his right hand outstretched. As he dives to grab at it, the shot switches to the side and it is his left hand that grabs the 'pearl'. The shot then immediately switches to a close up of his face and you can again see his right arm outstretched. (01:54:30)
Continuity mistake: In the hotel suite scene, when Mason has thrown Womack outside, Godspeed is aiming him a gun. At the beginning you can see it's a Beretta 92 but when he says "please, don't" and the shot changes, the gun becomes a Colt 45. Then the shot switches again and Godspeed is again holding a Beretta 92.
Continuity mistake: The deadline is at noon, but when Goodspeed is running to the lower lighthouse after the shootout with Hummel's guys, the skyline is either dawn or dusk.
Continuity mistake: When the SEAL team is onboard "Raider one" the pilot says "we're going dark" and SEAL commander gives them order to turn nightvision on. However, when camera shows the chopper from outside, there is a beacon light flashing in its tail. Trained Navy SEALS would never overlook this detail under any circumstances.
Continuity mistake: After the shower room scene where everyone's killed, Hummel and his men are checking out the bodies. They find a soldier who is still alive. Hummel then speaks in the camera on the marines left soldier. The film then cuts to the command center in San Fransisco. A man looking at a screen points at it and says "Look at this." In the shot, as he points to the screen you can clearly see it as being a radar screen, but in the next shot it turns to the screen with all the marines' camera's views on it.
Continuity mistake: After Goodspeed grabs the pearl on top of the lighthouse, one of the remaining soldiers shoots at him from another rooftop. When he starts firing, he's near the corner of the roof. But, when Mason gets up the roof, the soldier is nowhere near the corner. I don't see why he would switch positions, since moving to the left as he appeared to do would make it harder to hit Goodspeed.
Continuity mistake: When Sean Connery kills the soldier telling Nicholas Cage to get on his knees at gunpoint, Sean Connery takes the rifle and rests the stock on Nicholas Cage's shoulder. In the wider shot when Cage takes hold of the gun, the stock is a slightly different style than the one that was on his shoulder.
Continuity mistake: When they fire the missile, they say its headed for the game in Oakland. The tracking computer shows it heading for the Oakland Coliseum but when its diverted it shows it was about to hit Candlestick park in San Francisco.
Continuity mistake: When Mason pulls Goodspeed out of the water in the next scene they are both completely dry hair, clothes, face but when Goodspeed is picked up his hair, clothes and face are wet.
Continuity mistake: In the beginning of the movie as Hummel visits his wife's grave, the rain changes from shot to shot, in some it's raining heavily, while in others barely at all. In the shot just before we see who's grave it is you can see blue sky behind Hummel.