I think it was tattooed. I saw a few German Shepherd puppies at a show a few months ago that had recently been tattooed and the insides of their ears were green too.
iluvpitbulls, it''s from the tattoo ink. his registration number is in his ear and it had gotten tattooed a day or two before we picked him up so the ink was still pretty fresh. You can''t wash the ink out you have to let it just grow out.