During the mortar fight with enhanced supersoldiers, I killed first big wave, but the second one did not triggered and they stood in front of the gate. Nothing helped to trigger them. They were unkillable. I had to relog, start the quest again and then everything ran smoothly.
I think the problem may caused the fact, I could not intract with mortars for a few seconds - player has to stand so close to them to interact. If you stand not close enough, you see small interaction symbol, but you are unable to start interaction. So I lost some time and first wave of supersoldiers got close to the building, one half of them in front of me and second half to my left side. It looked like those on left side had some pathfinding problems. I killed them all by mortar, but the second wave was not triggered and they did not move from the gate.