This might be a possibility?...
I had come home from work one day and my husband was concerned because Chip had these little dark pimples on his belly. Chip has never had fleas or any skin problems. He said he just couldn't figure what it could be. He said he thought they were fleas, but he couldn't pick them off. So I asked him to show me.
Well...I was relieved to find that there were no fleas or skin problems. My hubby was trying to pick off his nipples!!

Boy was he embarrassed!

We both just died laughing! They are very tiny and I could see where he might think they were something other than nipples.
I hope that it is something as simple as this and that there is not a problem with your baby.