We have a 2012 Prius III that developed a water leak in the upper part of the rear hatch. The water would collect into the upper trim and would leak into the car when we opened the rear hatch. After looking at the issue for a while I discovered that the window washer nozzle on the upper part of the rear hatch had been pressed in slightly and it deformed the metal around it. So I removed the nozzle, pushed the metal back up, and put some silicon caulk around the inside and outside of the washer nozzle. It's been months now and no more water leaks. Just posting this in case anyone else had this issue.
I just noticed that I posted this inadvertently to the main Prius V forum. I'll repost this to the Gen3 forum.