Continuity mistake: When the President holds his frightened daughter, in the shot after the alien craft creates a shadow over the White House, there are photographs and a bust of Lincoln on the table beside the President - the view of the photos is not blocked by anything. In the very next close-up of the photos, things differ, such as a large framed photo of the President with the Dalai Lama that appears out of nowhere, between the photo of the First Lady and the photo of the Pope.
Factual error: In any explosion the shock-wave will travel ahead of any debris thrown by the shock-wave. During the attack scenes there are numerous cases of debris, particularly vehicles, travelling and landing in still air ahead of the arrival of the shock-wave.
Other mistake: When they're shooting the nuclear-bomb at the space craft for the first time (when it fails due to the shield on the alien space craft), you see that the airplane shooting the missile is breaking off to the left just after it's fired the missile. On the radar a few seconds later you see the airplane breaking off to the right. As if the radar displayed a mirrored view.
Visible crew/equipment: At Area 51's main research facility, Dr. Okun walks up to greet President Whitmore and as his assistant, Dr. Isaacs walks up behind him, the green actor's mark is visible on the floor - he even glances down at it. (Only visible on fullscreen DVD.)
Visible crew/equipment: At the containment lab, just before Dr. Okun unlocks "the vault", three actors' marks are visible. One mark is at the top of the ramp and the other two are visible just past the ramp. (Only visible on fullscreen DVD.)
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: When Jasmine grabs Dylan out of the car, his sneakers are white/black with black laces, but when she is kicking the maintenance door, his sneakers are white with white laces, then it switches again in following shots.
Visible crew/equipment: At the Area 51 lab, when President Whitmore is down on the ground in pain, in the shot from inside the lab facing the lab's outer hall, the alien costume only reaches just above the crewmember's waist - the costume straps attached to his pants are visible, as well as his arm. (Only visible on fullscreen DVD.)
Factual error: When the alien ship over New York blows up the Empire State Building you see the blastwave spill out in the street in front of the Empire State Building. This is in that part of the city that's built in a grid pattern. In front of the Empire State Building there's just another building, not a street where the blastwave and debris can spill into. All the people who are way down the street, looking at the building being hit by the beam just can't be there. (00:47:00)
Audio problem: When the Knights deploy their missiles with no results, we see in close-ups as they respond that Steven is Knight 1, Jimmy is Knight 7, and another Marine is Knight 3. After Steven says, "Knight 1. Sweet Luck. Echo, Fox 2," we see a close-up of Knight 3 and hear his voice (not Jimmy's) say, "Knight 7, Fox 2", though he is in fact Knight 3, and Jimmy is Knight 7. (01:00:45)
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)
Factual error: The US Bank Tower's placement in between Citi Group and Melon Bank is inconsistent from its real life position. Citi Group should be roughly directly parallel, not off-center at an angle.
Continuity mistake: When Jasmine sees the approaching fireball she grabs Dylan from the car and begins to run. In the shot from behind, there are double-yellow lines on the road at her feet reaching into the distance, but in the shot facing her the lines have vanished, though she did not change lanes.
Factual error: When the aliens attack Novosibirsk, Russia, a map of "Russia" in Russian letters is displayed on-screen from what is supposed to be a Russian news broadcast. In fact, it's a map of the Soviet Union, St. Petersburg is incorrectly labeled as "Petrograd," Moscow is too far east, and Novosibirsk is very badly misspelled. (00:15:20)
Factual error: El Toro base is shown being at the end of a long desert road. El Toro is in the middle of completely developed cities in Orange County. The desert is about 50 miles away over a few mountain ranges. (01:17:50)
Factual error: When the Empire State Building gets blown up, look to the right of the picture. The building next to it is the Citicorp Center. That is not right because Citicorp Center is on Lex between 53rd and 54th, while the ESB is on 34th and 5th. (00:47:00)
Visible crew/equipment: When President Whitmore, General Grey and the rest return to the containment lab to see the live alien, Major Mitchell stands directly in front of the smoke filled lab and the camera equipment/crew are visible in the reflection on the glass. President Whitmore, General Grey and a few others are supposed to be the only ones in front of the three aliens' liquid chambers. (Only visible on fullscreen DVD.)
Factual error: In the opening scene, the plaque from the Apollo 11 landing is shown sitting in the lunar soil. The actual plaque is mounted to the landing module, right under the ladder. (00:01:00)
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)
Factual error: When the alien ship arrives in Washington DC, its shadow goes over the Lincoln Memorial from the bottom of the Lincoln statue to the top. Since the saucer is heading over the National Mall and the Lincoln Memorial faces the Mall, the shadow should have gone from the top to the bottom. (00:21:40)
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.