In the commander mission: "Hunting the Hunted", in the ground part, if you go and rescue the 4 hostages in the cave before you have talked to Peterson (the 5th hostage who is on his own and talks to you about various things), then you will get a message like "Hunters, attack!" after you rescue the cave hostages, but nothing will happen, then you will go and talk to Peterson and he says he won't beam to the ship because you haven't rescued the other hostages yet, then you will walk round being confused, knowing you have to defeat the Alpha dude but he won't appear.
You can progress, as I did, by beaming back to ship then selecting to continue the mission. This will automatically put you in the cave and the attack will commence and you get to kill the enemies and final Alpha dude as normal.
Also is it normal for your crewmembers to disappear far away on the map and for you to be on your own against packs of enemies in I think it was the third energy bubble (the ones you keep transporting to, before you have escaped by turning the energy fields off) ? Or maybe they all died and came back from the respawn point, or something, but I doubt it. Also crewmembers often get stuck in the hostage cave or in its entrance arch.
Encountering bugged missions like this makes me sad because it spoils an otherwise superb game which I am really enjoying.