YES!
This ALSO happened to me. I must've replayed the check point over about 5 times, clearing the entire alien wave, only to get to a black hawk somehow intact with half of it in rubble half of it out of rubble.
This part of the mission is bugged, and also my whole campaign progress seems to be have compromised. Everytime I resume game it goes back to this bugged point, disappointing if I have to start again, that was a few hours in. But yeah when the waves get cleared and I move to the LZ, the marines still just stay in the zone where they fought the aliens screaming "MOVE OUT, GO!!"
This among many other disappointments with Crysis 2, brings a tear to my eye.
