Update:
I looked at the wheels up close with a magnifying glass, and the spots are most certainly through the chrome and embedded into the wheel finish. If I use my fingernail I can feel the edges of most of them. I still cant feel them with my finger. So I think I am going to see where I get with warranty. Hopefully there is something wrong with the plating, and if I do get new ones this wont happen again or not so soon.