Recently, there have been a lot of problems with poor quality imported, polished porcelain tiles, usually from china. Even though various sealers have been specified to use prior to grouting/walking on, the tiles have not been sealed properly causing staining problems.
I don't know from your question where the tiles originate from or how much they cost, but from experience, I have never had any problems with good quality spanish or italian polished porcelain.
By the sounds of it, you'll be lucky if the stains can be removed as they have penetrated into the pores in the tile. There are various products on the market from manufacturers such as Hagesan or Lithofin that may or may not work.
If it doesn't work, the liability may lay with either the tile supplier or the fitter, dependant on what advice you were given when you bought them. ie:- if the supplier said they should be sealed before walking on/grouting and the fitter knew this, then it's the fitter's fault. If the supplier stated they didn't need any treatment, then the liability will probably be with them.
If you do have to replace them, go for a better quality tile (obviosuly they'll be more expensive!) that doesn't need any type of impregnating sealer.
Hope this helps!