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 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: 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: The alien saucer that arrives over Los Angeles is said to be approaching off the California coastline, yet it is specifically shown approaching from Imperial Valley, which is to the east/southeast of Los Angeles.
Continuity mistake: At the MCAS El Toro ruins, when Steven's chopper is heard overhead, the First Lady sits up and leans on her right arm with her left arm over the blanket. In Jasmine's close-up, the First Lady is lying down fully covered by the blanket, but when it cuts back to the First Lady her position is back as the first shot.
Continuity mistake: When the B2 releases the nuke it banks away to the left, however the next radar shot shows it flying away to the right.
Continuity mistake: When Will Smith and Jeff Goldblum are in the mothership, Will says that once the missile is fired they have 30 seconds to get out of the ship before it explodes. The sequence of events, portrayed in real-time, from the start of the countdown to the detonation is 93 seconds. By the time 30 seconds has elapsed; they are just barely getting to the inner-triangle opening, with 23 seconds remaining. From here, it takes an additional 40 seconds to traverse 'the triangle' and exit the ship; with another 10 seconds passing after clearing the doors. The timer now shows 10 seconds remaining. Basically (according to the countdown), the first 30 seconds were depicted as being only 7 having elapsed; and the 50 seconds after that being only 13. Everything was in real-time. (02:18:25)
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)
Continuity mistake: Near the end of the film, when all the main characters pull up in a jeep to meet David and Steven who have just returned to earth, Jasmine leaps out first and is shown running alone toward them, yet Connie gets to the men first. This cannot be explained by Connie being faster than Jasmine as the distance is too short(the rest of the group stroll to the men in only seconds). Connie would have to run like the wind.