Window Alignment

I changed out the driver's door window motor. Pretty much plug & play. However, the top, right hand corner of the window (facing the door from the outside) weather seal gets caught behind the window instead of over the window like the other part of the weather seal.
I ended up having to remove the glass from the entire door to change out the motor w/o assistance and from what I see, it just sits back into the nylon attach pieces and bolts down.
What did I do wrong and how do I get the window to seal properly?