Sorry, but it's just your standard, everyday, run of the mill environmental damage. Copper is a very reactive metal and there is a lot of nasty stuff hanging around out there just waiting to make friends with those atoms.
I don't think you can tell how far the stain penetrates without cutting into the coin. The environmental reactions are on the surface and at best, probably penetrate less than a micron. This is not the same as dirt or verdigris that leave a raised surface.