Have you tried or applied anything to try and remove it. I know for a fact, any crap that sits too long on the paint, like bird crap or even a wet leaf can etch the paint and leave a mark. I can usually polish it out though. I usually use Adam's polish, but I found really good results by using a clay bar, 3M's scratch remover followed by a fine polish, then applying a new coat of wax. Not really sure what your situtation is without seeing it in person, but I would at lease give the clay bar a shot. It might even be iron deposit, in which case you could give
Aquartz Iron Cut a shot.