passenger window seems to overshoot and go over rubber seal on 1999 Mustang coupe

I noticed that if I close my passenger door on my Mustang with the window up, the top of the glass seems to go on top of the rubber seal - leaving a gap between the glass and the seal on the side by the pillar. If I close the door with the window down a bit, and raise the window after the door is closed from the inside, the glass seems to go properly with the seal being properly on top of the glass, and no gap on the side top. I ordered new seals from LMR, but looking at the seals they seem pliable and good.
I also notice occasionally the passenger door is a bit harder to close than the drivers, though everything seems to line up properly, pinstriping, door edges all look properly flush.