Continuity mistake: During the scene in the mall when the girl is in the dressing room, she keeps putting on more layers of clothing. But as they are shooting different shots she will have a hot pink shirt on, then it is back on the hanger, and then back on again. It switches back and forth many times. (01:00:50)
Other mistake: At the very beginning of the movie, when the guy throws the match into the house, it doesn't enter through the window. The match crashes and bounces back, but the fire inside the house still occurs. (00:02:40)
Factual error: At the end of the film, when Duchovny and Jones are on the ladder truck shooting the head and shoulders, they are yelling "go go go". They slide down the ladder and the next shot is the fire truck speeding away. Movie elapsed time 5 seconds. It is a physical impossibility for a fully extended ladder to be lowered, retracted and bedded in a span of less than 4-7 minutes. Even if the hydraulic lines are cut, the ladder would remain upright and not collapse/retract. (01:32:59)
Continuity mistake: Opening scene - meteor smashing into the car and you see the windshield flying out. Next day, character is driving the car and viola the windshield is still intact. (00:03:46)
Continuity mistake: When Dan Akroyd is discussing the aliens with the military, the digital clock behind him reads different, non-consecutive, numbers each time they show it. (01:07:55)
Continuity mistake: When Ira and Jones break into the secured area to get the specimens, they lay down in front of the barbed wire. Ida is wearing a black Colonel Uniform and Jones is wearing a Private Uniform. But when they get inside the facility Ida's uniform is clean and has no dust marks. (00:34:01)
Revealing mistake: This film was shot in Page Arizona with is pretty far north in the "high country". When they first drive up to the meteor side, there is Saguaro cactus that are only a couple of feet high with huge arms and a neon greenish color. These only grow on the desert floor in Arizona and they certainly are not neon colored. Additionally, the arms don't start appearing until they are much taller as they grow them to balance themselves since they have a very shallow root system.
Plot hole: On the doors inside the white dome, and on the elevator door, it is marked "Vapor Lock." This is impossible due to the mine shaft opening. It can't be vapor locked when there's an opening. (00:35:00)
Factual error: The aliens are supposedly nitrogen-based, making them vulnerable to selenium in the same way humans are vulnerable to arsenic because we're carbon-based. However, nitrogen atoms don't have the valence real estate to form the long molecular chains critical to the DNA structure shared by terrestrial and alien life (when Ira first analyzes the sample, he finds DNA with 10 base pairs). (01:20:30)
Continuity mistake: During many scenes of the movie, you can notice that Orlando Jones has no glass in his glasses at times, then does at other points. When they are in court, he puts his fingers through the frame to rubs his eyes. [Some people have said they're meant to be fake in order to make him look clever, but they've definitely got glass in some scenes.] (00:32:31)
Continuity mistake: When Julienne Moore's character trips over, from the distant shot she gets up onto her hands and knees, then when her garter is seen, she is lying flat on the floor again.
Continuity mistake: In the scene near the end when they first drive under the thing in the fire truck and it 'passes gas' on them, Orlando's glasses disappear during the 'passing' and then reappear a couple of shots later. (01:26:50)
Continuity mistake: When the guy on the green is waiting for his date, the champagne bottle mysteriously changes places. When setting the bottle down the lights from above change angles when he's walking to wash off the spillage. (00:45:20)
Factual error: The movie is set in Arizona, and at the end they say that the army will drop the napalm at noon. Granted they go a little early, but it should still be pretty warm, but, you can clearly see their breath as they talk. (01:27:25)