Auto manufacturer's rust warranties are BS. They are called 'perforation' as in rust-thru, not surface rust. The BS thing about it is that the rust has to go all the way through in order to make a claim. In most cases, the warranty is up before the rust actually goes all the way through. And who in their right mind would let the rust get that bad anyway? So you end up fixing it on your dollar.

EDIT: Try reading into whether or not there is some sort of paint integrity warranty. You may be able to argue that the paint peeled off due to abrasion from ill-fitting panels and then the rust formed. You cannot claim paint/rust issues do to wear and tear like rock chips but you may be able to if it is a design flaw or assembly/fit & finish issue.

 

Manufacturers rust warranties are for preforation, which would mean there would have to be a hole from one side to the other... You could take it in to the dealer and try to see if they could do a warranty claim due to appearance. I've seen this done before, though it's no guaranty, it's worth the try. There's marks idea which also could work, claim based on abration due to incorrect fitment of panels, causing consequential damage.