I might be thinking about the Camaro but on one of the cars, there is a metal bracket with a felt pad on it inside the door, on the inside of the window area. It keeps the glass 'located' so if you push on it, it doesnt slop around in the door (since we don't have 'window channels' like framed doors have).
If that's how the stangs are and the soft pad fell off, you will have metal scraping your window.
It'll be real easy to figure out. Just remove the door panel (with as much as you screw with your car bud, it probably takes you 20 seconds to remove the panel). Then with the window up, look right below the scratch to find what's scratching the glass.
I once did a temporary fix like this with a little piece of soft carpet. I glued it to the metal. A little piece of Microfiber towel would probably work decently. Fold it over several times to give you good thickness if you can.
Good luck bud.