It was happening in turn based strategic as well, I set the ship strategy to don't get hurt and it never moved anywhere near the planet, Had DUC I on it. I haven't tried quiting then restarting, I'll see what happens tonight.
Last night I tried shutting the game off during combat to see if this would stop the facilities from being destroyed. It does not change anything. Also combats in other sectors and by other races don't make a differance. I also sent an unarmed escort to a planet that had one facility destroyed several turns earlier. The unarmed ship was able to cause this as well.