It can actually come to the dealer with these spots. They are referred to as "rail dust" as it is usually caused from the fine metal particles that come from train wheels running on the track. It will embed itself into the paint and later rust. My white truck had it all over. The best way I have found to remove it is to use a Clay Bar. It took more than one time for mine. The spots appeared to be gone, but came back. The second use seemed to remove them all. It is alot of work, but it is worth it.
I reccomend staying away from the use of a buffer. In untrained hands it can do alot of damage QUICK. Also with the buffer you are removing a minute amount of paint (clearcoat), where as the clay bay supposedly simlpy "pulls" out the contaminants.