after you pull up your old carpet,it's common to find stains,they can come from pets,plants that were over watered.to some one that spilled the ice tea.are you sanding off the old finish,if so ,most of the stains will disapear,for the hard ones,talk to a hard wood supplier,they can provide a cleaner or wood bleach,good luck

You will be using a floor sander on this so like other said will probably come off.