I'll tell you exactly, precisely, specifically why you are dying. It is because Bungie made garbage programming. It was happening to me also. You know why else it is garbage Bungie?, because you haven't made an update for this either.
What is happening is that 1) you activate the 'Boomstick' skull that has it that any non-player blow up 5% of the time, 2) the civilians actually make it to the cargo ship, 3) whether they die or not, simply the act of them BOARDING the ship damages the ship extensively.
No ennemy has to be around. IT is is NOT a megaturret. The civilians are killing their own ship. Call it glitch if you will.
It's funny/frustrating because I saved right before a point where a bunch of civilians are coming to board the last ship (number 2), and even when I use my missiles (leader power) to kill some of them, and try and use my soldiers to block the path to the cargo ship - they get to the ship, and they blow it up. I have to restart, and not have that skull on.
So yeah, thanks for wasting my time Bungie - many others would swear for the wasted time.