David Levinson: I've had years to get us ready. We never had a chance.
President Whitmore: We didn't last time, either.
David Levinson: That's...definitely bigger than the last one.
David Levinson: They like to get the landmarks.
Kid on Bus: My dad said your son never went to space and it's just a conspiracy.
Julius Levinson: Oh yeah? Your father's a putz.
David Levinson: What goes up must come down.
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.