Nail holes are showing black stains

Q: I recently bought a house and pulled the carpet off the floors. There were beautiful hardwood floors underneath. I pulled the carpet tack strips off carefully from the edges and filled nail holes with wood putty. I applied an oil-based polyurethane and the floors turned out nice. However, as time has gone on (3 months) several of the nail holes are showing black stains around them that were not present at the time of finish.

Do you know how these are caused? Also, is there anything I can do at this point to get rid of them?

A: The carpet had probably been shampooed in the past and moisture collected around the nail and left the black water mark. You can recess the black area with a nail set and fill with colour match putty. I like the tube filler/caulking from Color Rite.