Door Damage caused by VW factory roof rack

I have a factory roof rack (made by thule for Volkswagon??)on my 2002 golf tdi gls (4 door). The paint is starting to chip off the inside of the doors... Is this a warrenty issue, anyone with any suggestions?

Pardon.........?????

You must be referring to the front mounts. On the 2000YM Golf the front tower mount straps are installed over an integral stud that is hidden by the rubber rain gutter cover. Is yours mounted thusly? I can't see how you could have damage unless the mounting was done wrong. The actual tower foot sits on top of the roof edge but it's the tower strap that pulls down on the foot. I would check the strap to see if it's attached to this hidden stud.