Continuity mistake: When David and Steven are on their way to the mothership, in shots facing David's right side the black safety harness and metal clasp are upside down, but in other shots the harness and clasp are on properly.
Continuity mistake: While David is talking to his wife, he holds the Johnny Walker bottle in his hand, then it is suddenly on the window sill.
Continuity mistake: When President Whitmore and the rest get to Area 51, you see David Levinson in the background. Right before they go through the doors, he has a sunglasses clip over his glasses. As they start walking down the ramp, they are still on, but right after the glass doors open, you can see for a second or two the clip is off the glasses. Then when they go for a close up of Levinson, you can see him take the clip off. (01:14:55)
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)
Factual error: When the nuclear bomb is released in Houston, the shot shows an interstate sign with South Houston as the control city. The only interstate running south of Houston is I-45, and Galveston is the control city on all its signs. (01:35:55)
Continuity mistake: At the SETI institute, there is a black guy on the phone in many shots, yet in one particular shot he is on the phone, but two seconds later he has jumped into a seat next to the woman and is typing. That's some pretty fast moving. (00:03:30)
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: When the alien aircraft at the beginning of the film first breach the skies over New York, when the camera cuts to peoples reactions, in all shots behind them the sky is filled with clouds, and when it cuts to the alien aircraft, the sky is blue. (00:22:55)
Continuity mistake: In the scene with Steven and David in the cockpit of the alien ship, as Steven hands David the cigar his fingers are close together in the shots facing him, but are spread apart in the shots facing David. (01:52:05)
Factual error: For anyone who is in the Air Force or has taken the time to go inside of an E-3 AWACS at an airshow you will note that the AWACS in the movie looks nothing like that of the real life version. There is no position in the back that they sit across from each other sideways as were the non pilots in the scene that the flame engulfed. The only crew that sits like that is the Navigator and Flight Engineer, but these two actors were clearly too far back for that. (00:17:40)
Factual error: When they show the Israeli Air Force with the Arabs, they show Israeli F/A-18s. The problem is that the Israelis do not own or operate any US Navy equipment - only equipment such as F-16s. (01:41:45)
Continuity mistake: In the middle of the film just before Steven Hiller crashes his fighter jet into the canyon, he looks at his fuel reserve, and if you watch closely the fuel reserve numbers just keep repeating themselves. (01:02:10)
Continuity mistake: Steve and Jasmine are asleep and the house starts to shake. There are 3 pictures on a night stand. Two of the three fall. When they wake up the 2 pictures are back up. (00:22:20)
Continuity mistake: At the beginning of the film, when the President is being briefed by his members of staff, there is a General wearing a blue uniform sitting by the left armrest of the couch, with his back all the way back touching the backrest. In the next shot, still by the left armrest, he is now sitting farther forward at the edge of the couch. (00:12:55)
Factual error: When we see the British pilots (with Iraqi pilots) responding to the news of a planned counter-offensive, the British pilot is stood in front of an F-16 with British markings on. This aircraft has never been in service with the RAF or purchased by the British government.
Continuity mistake: When Jimmy and Steven climb into the F/A-18 cockpits, there are various stickers on the backs of their seats which completely differ when they are airborne. (00:58:20)
Continuity mistake: Air Force One's cabin window shades move up/down when President Whitmore and Connie are talking, beside the President's sleeping daughter, and when the President asks General Grey for an update about his wife's whereabouts.
Continuity mistake: After their daughter leaves the room, when the President tries to lie to the First Lady about her condition, her hand is touching his face in the shot facing her. In the next shot facing him, her hand is down holding his hand, but when it cuts away her hand is back up touching her husband's face.
Continuity mistake: At the start, when the SETI Chief arrives at the lab (after being awakened), a SETI tech sits on the desk in front of the window blinds, which are pulled up (shoulder height). Next shot facing him, those blinds are pulled all the way down.
Revealing mistake: At Area 51, when the president's entourage fire their guns at the alien, the stunt wires attached to its upper body are visible, pulling the alien backwards. These stunt wires have nothing to do with Dr. Okun's medical equipment.
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.