I have a similar problem where if you fire a laser carbine (may be other weapons as well not tested yet) at a target you are garaunteed NOT to hit (too far, too much cover etc) it will play the sound effect but the weapon will not actually fire, and all soldiers can no longer be commanded. only way to continue is to end the turn.
I've also found a few of the ground terrain that is causing the hunter to crash in the desert base level.