I don’t have an exact reading on the humidity levels at this very moment but they don’t move and can’t be scratched off.I don’t think it’s scale rot but I can’t tell exactly what it is I believe if was scale rot It would spread out from that one little scale and become a bigger patch and eventually blister and seep and fall off. Normally it’s caused by either to much humidity and wet substrate or bacteria can be spread by mites. Do those black spots move or can you scratch them off gently obviously? Do they come and go in different places? He may have mites when you adopted him what are your humidity readings in the enclosure? I kind of doubt it’s mites they are not very common in bearded dragons but if he was around other reptiles like snakes it’s a possibility but very low.
What causes bearded dragon scale rot? What are the symptoms? How to treat and how to prevent scale rot in bearded dragons?thepetenthusiast.com
Here’s an article on scale rot there are lots of others I’m sure you’ve read lol. My dragon has some black spots like that and I think it’s just a pigmentation thing and scales just turn a black color as to the reason I’m not sure?