They all get the black marks which can generally be cleaned off but sometimes can start to rub the finish off. Cleaning the bag seals helps with that some. My TM is a 1996 so I don't know if you have the same hardwear as me but I got a big scratch to the left of the door on the rear shell that went through the striping design. I brought it to a dealership for a once over after buying from a private party. There are drop pins with a big finger loop (shaped like a "q") to secure the lower door at the hinges. They did not flatten those pins before closing and that finger loop dragged across the rear shell leaving a big arched scratch.
Not much help, I know, but that's my story.
Cheri