Audio problem: After the President tells General Grey that he is a combat pilot who belongs in the air, Major Mitchell says, "Okay, sir," but his mouth movements are not in sync. (01:57:40)
Factual error: When Russell enters his F/A-18 during the final assault, he pushes the keypad "8" button out of curiosity and it inadvertently arms a missile. In reality, the keypad buttons are merely for navigational purposes and map coordinates. They would never be tied to the weapons system. (01:59:15)
Continuity mistake: In the Area 51 hangar, when Steven and David are trying to take off in the alien attacker, we are clearly shown how the ship flies: Pull back on the controls, you go forward, push forward on the controls, you go in reverse. Later, in the mothership, after they have launched the nuke and are released, Steven pulls back on the controls, which should send them flying forward, but the external shot shows them flying backwards. (02:00:25)
Continuity mistake: After the shields of the motherships have been taken out and the fighters fire their missiles, we can see that the inflict a lot of damage to the mothership's front, but when Russell Casse blows the ship up that damage is gone. (02:00:55 - 02:24:45)
Continuity mistake: When General Grey tells the President not to engage until they have visual, in the President's close-up the exterior of this F/A-18 Hornet is quite different than what was shown in the earlier shot, as the canopy closed over him. All the rivets around the canopy have disappeared and the 'danger' triangle is much closer to the name Patrick, the seat differs, etc. Plus the fact that the canopy and hull are actually one unit in the second shot. (02:02:15 - 02:03:15)
Continuity mistake: Several times during the last air battle, the President shoots his missiles, but a view of his plane shows that it still has all four missiles. (02:03:25)
Continuity mistake: When Russell boards the F/A-18, he places the photo of his kids beside the left DDI on the instrument panel, which is to the left of the number key pad, below the HUD. When he says, "Payback's a bitch..." there is an upside-down matchbook cover (with the words, "Amraam armed....is off" scribbled on it) exactly where the photo was - beside the left DDI, but then later the photo reappears. Also note that the yellow/black zebra marker behind the photo becomes a blue marker as well. (02:09:10 - 02:13:30)
Other mistake: At the end, when Steven and David's ship is released from the clamp in the mothership and are leaving, Steven never puts on his seat belt. Surely from all the twists and turns, not to mention the little nuclear explosion, he would have been tossed around just a little. (02:10:30)
Continuity mistake: The airplanes they are flying have 4 missiles, yet at the final air combat the President fires 5 missiles: the first missile hits ship with the shield on, the second and third hit the ship directly, the fourth kills a fighter alien craft, and the fifth shoots at the green light from the main ship. (02:12:15)
Continuity mistake: After the President fights the Aliens in the fighter plane he lands to see a lot of people cheering and happy. If you look at his hair when he is walking through the long white hallway, it is messed up and not perfect. A second later, when he walks into the "Command Centre", Connie and Jasmine ask to see if their husbands are okay, if you look at the President's hair, it is now slicked back and perfect. (02:13:10)
Continuity mistake: In the scene at the end of the movie where David and the President are making amends, as you view the President from David's POV (face on) his head is tilted to his right shoulder, however, as you view the President (from behind) as he is looking at David his head is tilted to his left shoulder. This is noticed each time the perspectives change. (02:14:50)
Continuity mistake: When Will Smith and Jeff Goldblum are in the mothership, Will says that once the missile is fired they have 30 seconds to get out of the ship before it explodes. The sequence of events, portrayed in real-time, from the start of the countdown to the detonation is 93 seconds. By the time 30 seconds has elapsed; they are just barely getting to the inner-triangle opening, with 23 seconds remaining. From here, it takes an additional 40 seconds to traverse 'the triangle' and exit the ship; with another 10 seconds passing after clearing the doors. The timer now shows 10 seconds remaining. Basically (according to the countdown), the first 30 seconds were depicted as being only 7 having elapsed; and the 50 seconds after that being only 13. Everything was in real-time. (02:18:25)
Visible crew/equipment: When Dr. Okun is about to unlock "the vault", and says, "The freak show," a crewmember wearing a black and white striped shirt is hiding under the vault's floor, right behind Okun. (Only visible on fullscreen DVD.)
Factual error: There is a shot of the Imperial Valley at night with the edges of the Los Angeles destroyer spinning over the mountains. The center of the destroyer is hovering over downtown LA. Imperial Valley is over 200 miles away from downtown LA, and the destroyer is no more than 20 miles in diameter. There would be no way the edges of the destroyer would extend far enough to be seen from Imperial Valley as shown unless it was over 100 miles in radius. The ship does not even hover over Steven Hiller's house which is in LA, it can nearly be seen whole from there. The destroyer would be obscured by the mountains and from 200 miles it would appear much smaller.
Factual error: During the final battle over Area 51, Russell Casse appears in his F-18 and states he is armed. After he attempts to acquire radar lock on the alien's primary weapon, he states he is locked on and has tone. He then says the tactical brevity code Fox-2, which indicates the launch of an infrared-guided missile. However, the missile he is actually attempting to launch is an AIM-54 Phoenix, which is an active radar guided missile, designated by the launch code Fox-3. The master monitor display also incorrectly shows the missile mounted on the port wingtip launcher of the aircraft where the AIM-9 Sidewinder would normally be mounted, instead of on the port wing's weapon pylon where the missile actually is. Historically, the F-14 Tomcat was the only fighter capable of carrying the AIM-54, as it was such a heavy missile; the AIM-54 was never used on the F/A-18. Instead, they carry the AIM-120 AMRAAMs, not the AIM-54 Phoenix that were shown in the film.
Visible crew/equipment: When President Whitmore returns to the containment lab to see the live alien, just as Major Mitchell and a Secret Service Agent walk to face the smoke filled lab, the actor's mark is visible on the ground as the Agent steps up to it. (Only visible on fullscreen DVD.)
Visible crew/equipment: After Dr. Okun unlocks "the vault" he explains the aliens' telepathic ability, and as David steps closer to the tanks the actors' marks are visible on the floor. (Only visible on fullscreen DVD.)
Factual error: David and Julius are traveling south to DC from NY so David can tell the President about the alien's plans. At one point, they're inside the city and the U.S. Capitol building is directly in front of them. This shot is famous because many movies have photographed the Capitol building from here. To get to this point in their travels they would have, in all likelihood, passed right by the White House since they are heading south on Pennsylvania Avenue towards the Capitol Building.
Visible crew/equipment: When Dr. Okun leads President Whitmore, General Grey, David and the rest to see, as he put it, "The big tamale," the red actor's mark is visible at the top of the landing as they all walk up the ramp. (Only visible on fullscreen DVD.)
Visible crew/equipment: In the containment lab, when the alien awakens and begins its attack, the alien moves from right to left towards a doctor, who is backed up against a door. The crewmember who is wearing the alien costume has on a white shirt and black trousers, and the costume's straps attached to the pants are visible, as well as some wiring at the back. (Only visible on fullscreen DVD.)
Answer: Remember that the aliens had to interface with our satellite computer code first...David simply "reverse engineered" the code to create the virus. When it was uploaded, they didn't have enough time to combat it.