In the Chaos campaign in co-op my friend and I randomly kept having ships die in the post mission screen. The first time we did the mission, all the non-flagships that were still in the mission were killed when the Blackstone fortress disengaged. We then reloaded and tried again by disengaging all of the non-flagships, and this ended with all of the ships that never even went into the battle dying.
We were able to get through this mission with no losses by bringing every ship into the mission, and disengaging every ship that wasn't a flagship. This caused a lot of warp events but resulted in no random deaths of ships. No idea what would be causing this.