It can also come from BP's sitting in their urates, whether on paper or substrate.
The rescues I got in that had scale rot, were usually kept in the typical "neglect" situations, bone dry enclosures, no optimal heat, no humidity. I have never had it in my own collection, just received it with rescues, but none of them were kept in wet conditions, although I'm sure that would make a better bacteria breeding ground ?
Hopefully the OP's snake doesn't have anything serious going on and with better husbandry, it will resolve.
edited to say, trying to find some sources, its interesting reading for sure !