I didnt think of much at the time, but during a mission when my squad was ganging a Sebelian non-com one of his reaction fires, which didnt hit, caused a rookie to panic for a turn. The odd thing was no one had died yet and no one had taken any damage for several turns if at all.
While your tweaking the morale system, if its not too much work, can you have message pop up whenever something actually reduces the troops morale? It doesnt have to say to who or by what amount, just that it happened and its cause.