Other mistake: Just before Patricia Whitmore's plane (no. 107) is shot down, it is briefly shown with its number mirrored.
Continuity mistake: At the end of the movie when the mothership takes off the central saucer section is in place, yet we saw the queen alien fly off in it earlier on.
Continuity mistake: Early in the film, as Jake and Charlie are towing a new weapon system to its destination on the Moon, we see Earth in the background, more than half illuminated by the Sun. Jake says they are 7 miles away and closing on their lunar destination (which should only take a matter of moments). A few moments later, as Jake and Charlie are still in approach, we see Earth in the background again, but it is now in a waning crescent, only 1/3 illuminated by the Sun. This would indicate over a week's passage of time.
Continuity mistake: When we first see Dr. Brakish Okun lying in bed the arm of the bed is up. Then just before he wakes up the arm is down. (00:19:45)
Answer: General Adams was only referring to the aliens in the Area 51 prison as having been in a catatonic state for 20 years, not all of the aliens that survived after the mothership was destroyed. Presumably, the aliens in the prison came from the City Destroyer that crashed near Area 51, but the aliens Dikembe fought came from the landed Destroyer, and with their ship intact (and given the fact that it was trying to drill to the core) those aliens retained more of a will to fight.
I don't buy that. After man kind fought the aliens the fiercest war it had known, it let an alien unit go on fighting an African militia for 10 years without providing help? I would imagine if at the end of the war there were still aliens with fighting spirit, world armies would be all over them.
There is a novel authorized by the filmmakers called "Independence Day: Crucible" that takes place between both movies. It explains that Dikembe's father fought a ground war against the aliens from the landed destroyer, all the while stubbornly refusing help from the outside world.