Is this in the tint? Scratches are caused by something digging into the window... So with the window down, I would take a tooth brush or some kind of cleaning device, and scrub the window felts. Maybe some compressed air (carefully) and clean as best you can.
If you hear a screeching noise when the window is going up or down it's not a good sign. Light sand from gravel roads and rain are the perfect storm for scratched side windows. Unless you can stay off gravel roads you have a chance of getting light scratches.