Is this the possible cause of water entering right-rear floorboard?
 

I lifted the car up and noticed that one of the 2-2.5" round black plugs that are connecting the side skirts to the body was missing. The missing one is right near where the water is located. I looked up in the hole and it does seem to be a possible entry spot. I just started getting this right after it left the dealership about a week & half ago. So if its possible then, they probably just knocked one off during its visit.

I don't think so. For one, how would water get upwards except for spray.....
 

and I had my skirt replaced a while back and one of those clips/plugs broke, I've had no water.

So far the only time I'm getting water is when i'm driving. I haven't proved it completely but .....
 

I'm pretty sure of it. I'm really just trying to combat any possibilities. And that was the first thing I saw when I put it in the air.

I had this same problem last year......
 

after 2 1/2 weeks in stealership they found a cracked drain hose for the sun roof. No problems since.