My subcontractor came back several weeks after the initiall sanding and staining of oak floors (some very old board, some new patched) to do the final buff coat.

We opted for a medium stain, not clear.

To everyone's dismay, the stain was coming off with the buffing in patches and spots. Everyone seems unsure what is causing it. It seems to be happening more where the new patch wood was used, and in higher traffic areas.

Was it not properly treated prior to staining? Or not sealed properly?
Resolution is to resand down all the floors, stain again, and reseal.

you need to make yourself a little more clear on this to be answered effectively/

what do you mean "stain is coming off in spots"

do you mean color (stain) ir do you mean the topcoat of finish?

also what products were used?

were they waterbased products (stain and finishes?)