Dear Vadium
I've had something similar happen to one of my client's floors. We discovered that the underpad beneath the area rug had black coloured foam bits in it and the colour was migrating into the floor finish. Solvent woudn't take it out so I had to sand off most of the surface finish and recoat that area. In the rare case the dye from the carpet will migrate into the floor finish but I've yet to see this and in this case there would no underpad. Change to a better quality underpad, or use one if there is none.
There is one more possibility and I've only seen this once in 22 years. There is a blackish blue fungus stain that is associated with oak. This will appear only when the temperature and humidty is just right for this organism to grow and leave it's coloured stain behind. In this case we had to resand the whole floor and to my knoledge it never came back. But they first appeared as dots no more than 1/4" in size.
I hope I have helped let me know what you discover. This is a very curious problem and I just love a mystery, just sorry it had to happen to you.
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As always your Most humble servant, Joseph, the Wood Floor Doctor.-