Can you see if the old shed skin has stuck around the edges of these black spots (in other words, does it look like the black spots did not shed)? Were the spots there before this shed? It is very hard to say what this might be as we can't see him. The main concern is whether these spots are fungus or infections. You could see if they come off with gentle rubbing...try flushing and rubbing with warmed saline (contact lens rinse) and a Q tip to see if they move or come off. It wouldn't hurt to dab a bit of Polysporin on them. This will treat an infection, protect and lubricate them. If they seem to get larger or if you see a rim of irritated skin around the edges go to a herp vet.