Im still in my heat gun roasting infancy, but the spots you mention sound a bit like what Ive heard others call divots. The explanation for these was the beans expanding to quickly and structurally something had to give. Generally in my experience these spots are little potholes that are almost perfect circles. Im assuminng these divots can be prevented by a slower more even application of heat.
The other black mark I have achieved :) are burnt tips ie tipping. Apparently if the heat is a bit too high the first part of the bean to give out is the thinner more easily burnt tips. Im not sure if tipping relates to the incorrect application of heat at a certain stage of the roast or is just simply an indication of roasting at too high a temperature from the start.
Either of these traits, while not being a desirable outcome, have not lead to a massive degeneration in the ultimate taste of the coffee in the cup.