There's no black substance on the lens from manufacture. Sounds like you're smearing the black paint from the lens ring onto the lens and getting confused as to where the black stuff came from. Unless some boob in the past got or put black paint on the lens.
There's definitely a school of thought that advises to "fill in" deep surface scratches with black paint/felt-tip etc. The idea being that light reflects and refracts weirdly around scratches, gives huge flare and lowers overall contrast. Filling in these scratches with black paint stops the flare but might show up as a very faint dark spot on a photo (depending on location on which element of course). So there might be some paint from one of these "fill-in" jobs.
Or yeah, you're just cleaning the paint off the rim and smearing it off the glass (or you're cleaning off the bits left by the guy before you who did that).
I'd suggest get a Lenspen or two, they'll clean anything off the glass (except coatings), leave no residue, and won't touch the rim paint.