rain collection at the right rear floor and under bench seat

My mechanic claims that the water is coming from inadequate seals in the car's right door windows and finding its way to the rear floor.  I have driven in a light rain, getting a collection of water, but not seeing it come from the windows.

I noticed a loose plug in the floor pan under the rear bench seat near the center hump.  i had thought that the plug filled a hole for the battery located under the rear seat in the bogs. I thought that perhaps the the water from puddles in the road was entering here and was prepared to seal the plug, but discovered that there did not seem to be an actual hole in the metal pan behind the fiber covering.  

Can somebody tell me where the water in coming from?

Peter H. Frink
Kennebunkport. Maine