Continuity mistake: In the motorhome, when Troy tells Russell that he feels sick, as the RV pulls over in the wideshot the back window curtain is open, but closed in other shots. (00:55:00)
Continuity mistake: When Captain Hiller begins his attack with the rest of his crew from El Toro, when we see the room where the General and the President are, a man says "Missiles have been fired", it shows on their screen a countdown of "metres to target". It does a countdown of 5000 to 4000 twice, and 4000 to 3000 twice. Also, when we next see the countdown before the missiles hit the shield, the last number is 49m, then the following shot of this number it says 107m. (00:57:50)
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: Just after Steven and Jimmy board the Hornets, aboard Air Force One, General Grey receives a call from Norad and when the crewman hands the General the phone he sits down, but next close-up he is still standing. (00:58:35)
Continuity mistake: Close to the middle of the film when Steven Hiller and his wingman Jimmy are running from the smaller alien aircrafts, Jimmy says, "I think I'll try something", and in this shot we can see Jimmy's fighter jet go up, and in the following shot, we see it go up again. (01:00:50)
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: When Captain Hiller ejects from the F/A-18 he is clearly strapped into his seat, but when he lands the seat is nowhere to be seen - it's not on the ground and he's not sitting on it. Then shortly afterward it instantly appears near him. (01:05:35)
Continuity mistake: When Captain Hiller is dragging the unconscious alien across the desert, the sky alternates between overcast and perfectly sunny depending on if it's a close up or far off view of Hiller. (01:07:30)
Continuity mistake: In the middle of the film when the President is in Area 51 looking at the alien aircraft, there is a shot from the back and you can see that the General is not standing really close to the doctor, in the following shot from the front he is standing side by side with the doctor. (01:14:10)
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: When David and Dr. Okun are inside the alien aircraft having a look around, it cuts to a front view of them, and if you look to the right two other scientists walk in. The scientist with the mustache and beard stops and looks, and the other walks a bit further and peaks over, then in the following shot you can see this action again. (Special Edition.) (01:18:20)
Continuity mistake: When Dr. Okun and David are inside of the alien ship, and Dr. Okun shows him the scrolling green lines on the console he says that they don't know what they are. David says it's the same thing as their countdown signal and they always move together. Yet when Steven is flying their ship through the mothership, the lines go horizontal, spread apart, and even turn blue in some parts. (01:21:00)
Continuity mistake: When David is looking for ice, the fridge door shelves are full of food. When Connie puts the bottle into the fridge, the door shelves are virtually empty. (01:24:55)
Continuity mistake: When David is getting drunk and he's talking to Connie, at one point he slams the bottle down on the counter and a little liquor sprays up out the opening. Then they talk for a second, and he picks the bottle back up to pour himself more, but he now needs to unscrew the cap which was just lying next to the bottle. (01:25:45)
Continuity mistake: At the end of the scene, when Connie tells David that she has never stopped loving him she is standing in a doorway. The close-up shot shows her arms are folded across her chest, but when it cuts to a longer shot her hands are on her hips. (01:26:10)
Continuity mistake: In the Area 51 lab, after the alien is shot, when Major Mitchell rushes over to Dr. Okun's body, his head moves closer to the monitor between shots, as well as other changes. (01:32:00)
Continuity mistake: After David looks in the fridge for ice, Connie appears at the doorway, and when he makes a toast to the end of the world, the bottle to his right turns between shots, note the label. (01:33:10)
Continuity mistake: When David removes the bottle that Connie put in the fridge, in the next shot as Connie says, "Research and development," the coffee filter behind her moves from the edge to farther down the table. (Fullscreen only) (01:33:45)
Continuity mistake: In the middle of the film when we see the President inside the command station, just after they hit the alien aircraft with a nuclear weapon, he turns to his side and says, "Call the other planes back," but in the following shot he is completely facing the guy he's talking to. (01:34:30)
Continuity mistake: After David makes a mess in the Area 51 alien attacker's hangar, when he is sitting on the ground facing Julius, the liquor bottle label changes directions in his hand. (01:35:25)
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.