I have the same issue with the little rear fixed window sticking out along the edge closest to the rear door. In my case it is the one on the driver side. It is definitely noticeable once you see it!
I have tried pushing it in but no luck yet. I will mention it to the dealer but I am afraid they might screw up something during the "repair".
I have tried pushing it in but no luck yet. I will mention it to the dealer but I am afraid they might screw up something during the "repair".