[A horse with no name]

Oops!..I just posted...That's that rubber boot that I'm referring to...Your window is lifting too high.

Post:
Yes...It very well could need adjusting; it appears that the window may be lifting too high...On the very top front of the small fixed window, is a small rubber boot...When up, is it lifting this boot up?..If so, it's the reason why the door won't shut properly with the window up...The correct adjustment, is when the top of the window 'just' touches the top of the outer seals lip.

2. Check to see if the small side fixed window is secure...If it moves, there are two screws on the outside on the channel - door jam, and one inside the door panel that will require tightening.

If the window needs to be adjusted so that the window stops at a lower point, that also requires the door panel to come off...There is plenty of posts that will show you how to take off the door panel, including how you adjust the window height.

Be careful not to break the plastic clips (+screws) that hold the door panel on.