Black marks on Aneros?

Have you tried an alcohol swab to make sure it is not some type of ink mark from quality control that made it through? My products don't have this.

I used to do molding years ago, that almost looks like the plastic burnt either in the mold or the injection nozzle. I would say that if you don't feel anything when slowly running a cotton swab over it, it most likely will have no bearing on use, but if it makes you uncomfortable send support the pics and they may send you a new one.

I wiped it with a cloth with warm soapy water and most of it came off, still a minuscule amount on there. Is it safe?

If you can make it clean- don't worry. I guess that it's just a residue from black plastic holder where your Aneros nestles. Probably it scratched this holder when you took it out or during transportation.