This situation has happen before, in older versions, as if the game is loaded, and all the civilians, are near to the aliens, then they will be killed, and you lose the battle, before you start, this should not happen. The civilians should try and run toward your troops, and safety, and not into the jaws of death!
The AI of the civilians, needs to be looked into, as the above situation can be very frustrating, Please have a look at this!!