Corrected entry: When the president talks to his wife who's in LA, he says he has a helicopter waiting to take her to Dulles airport, which is in Virginia. Then the General maybe 30 mins in the air after the attack says the helicopter never made it to Dulles. That's 2,444 miles - an average helicopter (which she gets in) can only go 250 miles before refuelling, they would have to refuel almost 10 times.
Corrected entry: When the president is in the air force bunker inspecting the spaceship, Dr Oken states that the scientists have been repairing it since the late 60's. The president says they've had it for 40 years and know nothing about it. That would mean that the movie would've been set in 2006 and not '96. (01:08:50)
Correction: No, they've had it since the Roswell crash in the 40s, he says they only figured it out enough to repair it since the 60s.
Other mistake: When David asks Major Mitchell if he can shoot the soda can, Major Mitchell has to ask a nearby sergeant for his sidearm, despite already having one on him when he shot the alien earlier.
Suggested correction: He probably shot his own gun empty or nearly empty, so he removed the magazine. They fired at least 10 shots at the alien, and he planted another 3 in it up close.
Corrected entry: How come the aliens keep attacking major cities on July 3rd? After the first attacks people flee the major cities and surely the aliens must have realised that reaction would come. So why blow up abandoned cities?
Correction: They want to destroy the infrastructure, thus making the cities impossible to live in. This action will eventually kill a lot of people (lack of water and food, spreading of diseases breakdown of healthcare and law enforcement etc).
Correction: Abandoned cities were being blown up because every major city contains what we call natural resources. Our gas, our oil, our source of power. When Whitmore saw their plan in his head he discovered that "after they've consumed every natural resource they move on" the aliens will not leave any city in the world untouched until they have taken everything from us.
Firstly our resources are not in our cities, especially not the center. Oil and Gas are produced and stored outside the cities, for obvious safety reasons. Secondly if they want our natural resources, they wouldn't be blowing them up. Thirdly, I doubt they are after our oil, considering what technology they use, I'm pretty sure they were after the water and oxygen for their spacefaring civilization.
Correction: The aliens don't know if the cities are abandoned or not. They just know that most people live in cities.
Corrected entry: Area 51 should be deep underground. The rocks should therefore provide everybody with enough cover for large bombs and even protection from the alien's primary weapon. When Will Smith and Jeff Goldblum go out to save the world in the alien spacecraft, the door to the surface opens. The launch site has its own door to the outside world. Why is it that the base is deep underground but has a big door leading to the surface that has no protection at all?
Correction: It's not simply a door into the outside, it's a launch tunnel at least one hundred yards long. There are heavy blast doors on the inside that are opened so that craft can exit, and it can be assumed that there are also similar doors on the other end of the tunnel. All this is a far cry from a simple surface door with no protection.
Correction: The Command Center is deep underground. Portions of the base are on the surface.
Corrected entry: The aircraft that deploys the nuclear missile at the saucer over Houston is a B-2 Spirit, a slow moving stealth bomber. It would have made more sense for the human command to deploy nuclear munitions using a more maneuverable fighter/bomber that stands a better chance of escaping the blast and any subsequent alien fighters that would be dispatched.
Correction: This supposes too many things, notably that the military was intact and had every aircraft at its disposal. We see the aliens struck the base at El Toro. Since we don't know what other bases, installations and aircraft may have been destroyed after the initial attack, we can't know what aircraft were at their disposal. Not to mention that the humans could have been hoping stealth would be an advantage over maneuverability.
Correction: The US Military is down to 7% as reported to Mr. Nimzicki earlier in the film. At that point, you use what's available.
Revealing mistake: In the exterior shot of Air Force One and its accompanying jets in the air, just before the shot of David getting nauseous aboard Air Force One, something suddenly comes up along the entire bottom edge of the screen. This is only visible on fullscreen DVD. (01:08:10)
Suggested correction: That is another jet guarding Air Force One.
Correction: He says "Nellis", not Dulles. Nellis Air Force base is about 250 miles from LA.