How tall are the coop & run?
You might check for feathers or blood on the top inside. I have read that if quail get scared and try to fly up, they can hit their head on the top of the coop and hurt themself. Feathers or blood might be proof if this did happen. No feathers or blood leaves you right where you were before, not knowing what caused this.
(I have no personal experience with quail, so the most I can suggest is "look and see." It might be a real thing to consider, or it might be an urban legend, and I don't know enough to tell.)