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)
Revealing mistake: When Jeff Goldblum is throwing a tantrum in the hangar housing the captured alien craft, he knocks over several plastic garbage cans, one of which is clearly labelled "Art Dept" - kind of odd for a top secret underground government military research facility. (01:35:15)
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)
Audio problem: After David's rant about burning the rainforests, etc, when he's on the ground Julius takes the bottle out of David's hand and we hear the sound of the bottle hitting the floor. But Julius still has the bottle in his hand, then puts it down two shots later - with no sound obviously. (01:35:30)
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)
Factual error: The missile launched by the B-2 is made-up. The nuclear missiles carried by the B-2 are powered by a small jet engine, not a rocket motor. The last air-launched, rocket-powered, nuclear missile was withdrawn from USAF service in 1990, before B-2s had even been delivered to the Air Force. Plus, these missiles are very accurate and have a range of hundreds of miles. Why get so close? Finally, the B-2 pilots have no flash blindness protection. No blackout panels on the windows, or special goggles that darken when exposed to bright light. The tinted visors on their helmets isn't good enough to block out the flash from a nuclear detonation. (01:36:20)
Continuity mistake: During the First Lady's death scene, Connie is on the First Lady's left, when the President asks his daughter to go out in the hallway. But in the very next shot, Connie is on the other side of the bed standing right next to the little girl. (01:39:55)
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: Just before President Whitmore gives his rousing speech, when Major Mitchell is talking into the mic, asking for all flight crews to report to their designated areas, the camouflage pattern on his uniform is entirely different from the uniform he wears in the previous and following scenes that he appears in. (01:51:20 - 01:55:10)
Continuity mistake: When Major Mitchell gives the crash course to all the new pilots, his hair his much shorter than in previous and following shots, and Russell's beard is also much fuzzier than it was in the previous shots, etc. (01:51:30)
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)
Continuity mistake: After President Whitmore comments to General Grey that the pilots look young and nervous, when Major Mitchell speaks into the mic and asks for all flight crews to report to their designated areas, the President climbs up onto the truck behind Mitchell. Next shot though, he is only just now walking toward the truck and then climbs up. (01:55:10)
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.