Are they reddish/brownish spots -- looking almost like dirt? Do they wash off? Could it be a little start of red yeast infection? The same thing that causes the reddish brown staining below their eyes sometimes?
http://www.dailypuppy.com/articles/h...f-605c17e69ef1
could also be ear mites:
Ear mites are small parasites which can invade your dog's ears. These mites typically cause a dry, dark brown debris to form in the ears of dogs. Ear mite treatments kills only the adult mites, not the nymphs, (pre-adults). Effective ear mite treatment includes an initial series of treatments to kill the adult mites followed 10 to 14 days later by a second series of treatments to kill the newly matured adults.
http://www.thepuppyplace.org/page46.html