I had a new top installed on my 2014 Convertible during the fall. I have noticed that I hear water swishing in the side panels where the back small quarter windows go down. I have had to use a shop vac after every heavy rain to remove the water and debri. What causes water to get in these spots?

 

There are drain holes down in the quarter panels under the windows. Water seeps down there from the 1/4 glass area and also funnels there from around the convertible top runoff.

Your drain holes are plugged up with grime, leaves, pine needles etc.