Sounds like you need to make an adjustment to the door, is it only the back corner that is causing this? If so, roll the window all the way down, brace the door on the outside with your body and pull on the window frame at the rear corner. I have spent many hours aligning the doors on my Milano, this is a good way to get the area around the window frame lined up. Pull hard enough to flex the window frame but not too hard to rip it off. Just play with it a little and you will get it right, try to make it even with the front the back door frame.
Thanks Sam. I pushed the back window frame with a lifting force and it is much better now. I still need to leave a section of the weatherstripping loose, just around the lock area, but this is the best I feel safe to get for now.
If there area is around the door closer, you can adjust the strick plate/pin out just a little, it is a allen bolts on the car, there is a good amount of adjustment in them, just be careful not to adjust up or down, takes a little playing with but I am sure you can get it to work right and make your life easier.