I've read somewhere not to stop the roof operation midway but I did by accident twice the first week without any issue - maybe you can stop it midway and look in the storage area to see if there's an object causing the abrasion? Or have someone with fast reflexes (like the karate kid) look and grab it while the top is lowering or raising.

 

One of the small straps that secure the top to the frame came loose and allowed the top to fold under the rear deck cover. That shape is an imprint of one of the stamped holes in the cover. Now to find the plastic attachment piece.