First, I am not an expert - however, based upon my chemical engineering undergrad degree, I have a few questions:

1. Did they use any tap water on the floor during this process? E.g., sometimes floor refinishers will "pop'" the grain using water - and then resand the floor.

2. Was any iron/steel in contact with the floor?

The reason for my questions is that it seems like there is a chemical reaction happening on parts of your wood floor. Impurities in tap water can cause oxidation and staining - especially if your water is high in iron. Also, when iron/steel comes in contact with oak, it can cause a blue/black discoloration (tannins in the wood react with the metal). Sometimes scrapers are sharpened - and someone does it over the floor - and little pieces of metal get into the grooves - and react with water.

If the answers are "no" to both of the above, the third possibility is that those boards contained a type of fugus - and the water in the finish "activated" it (similar to soil - there are different types of fungus that can become an issue if a container/pot is overwatered). My understanding is that this fungus is pretty rare. It can be addressed by scraping the spots off (after sanding) - and using a neutral oil based sealer before using a water based finish.

Again, I am not an expert - just using some of my undergrad knowledge (I'm an attorney - so, I don't use it on a daily basis).

If, the floor was previously stained. It can be stain deep in the grain that cannot be removed bleeding out. i would just color it in with a touch up marker or tinted poly with whitener in it.

Thats the risk you take on a refinish. Especially when trying from a darker to a super pale look.