I'm having the same issue in my current game... when I placed the prospectors near a depleted patch, instead of turning the depleted ore into new veins, new items seem to spawn in the ground marked for deconstruction.
Inspecting the depleted ore patches the other mod that seems to be affecting it is Alien biomes, not sure if that's significant or not.
Also, I'm running a Angel & Bobs game atm, and I'm running low on coal on the starter patch, so I kinda need the prospector to work, else this run will be dead very quickly :(