Hey, if you are an unarmed civilian and someone start shooting around you, I bet you will prone!
OK, let's serious...
Yesterday I set up an intro and I found your problem, but my civvis go prone when they are at peace (no shooting). They were standingfront of a wall and behind them the armed insurgency. And the civvis randomly go prone and stand up. They were:
* setbehaviour "careless"
* setunitpos "up"
* disableAI "move"
Finally, I noticed, they do it only in the begining of the mission. So I inserted a landscape scene before the execution, and when the camera go to the wall, they just stand as I want.
BUT! When the bad guys start shooting - of cource - they try to prone, but they are dead before they can.
In my case, it's more realistic.