I saw this happen to my ship last night. (No screenshot.) The context seemed to be that I'd taken out their drone system on the ship, but they repaired it and reactivated the drone. The drone's first shot after reactivating is what hit my ship through my shields.
I was playing one of the Osprey and had only two levels of shields at that point. The shot hit toward the front of the ship, like weapons or scanners.
I'm not sure if it was actually the reason or just happenstance.