Welcome to the MMMV, sorry to hear about your issue. I can't see any of the issues from the picture you posted, but generally paint doesn't come off unless some kind of chemical is applied to the Minimate. Soaking Minimates parts in soapy water prior to painting them is common place and rarely results in missing paint.
Thank you for the greeting! I just labeled the part with no paint with a red circle, so you can see it. Compare that to the normal flesh color.
So a chemical might have taken the paint off? I think I washed with regular water. I hear that rust can cause MiniMate paint to come off.