If you look up door glass for 65 GTO convertible, and hardtop, they do not use the same glass. Likely you have a convertible door on a hardtop body. The sheet metal and vent window interchange, but as I posted, the door class is too short. Running the window regulator up too far tears up the seals in the door as has already been described.
Also if you google image of 65 GTO, and look at the side view you can see the opening of a convertible compared to the vent window of a hardtop is lower due to the folding mechanism taking up more room in the roof.
It was 50 years ago when I swapped the 63 Catalina doors between a convertible and hardtop, but the result was the same. Swapping the glass enabled me to use the convertible door on the hardtop body.
