M.K.
My husband and I have been a homebuilder for nearly a decade building tracts of home in Phoenix. I have owned three homes with granite countertops. There is always some inconsistency in granite because it is stone. It is formed by the hand of God to be a perfect part of a mountain not to be a luxury finish in your kitchen. It is consistent for there to be imperfections in the surface for example, small areas where the surface feels slightly rough because there was a void in the stone. Granite is polished to create the beautiful finish so you could be looking at a polishing imperfection or it could be part of the stone itself.
If you think you may have gotten poor workmanship in creating the finish and you have a defective piece of stone from that perspective you may be able to have somebody come out and re-finish the granite, basically grind the finish off and re-polish it, this would more than likely involve the entire slab if not the entire kitchen. If the cloudyness/inconsistency is part of the stone you're probably less likely to get any solution because your contractor would have to get another slab installed. I'd say you're going to have to raise quite a stink to get either of those things done.
The contractor should have had you choose the actual slabs yourself, then you wouldn't have these types of issues. If you did choose them you're probably completely out of luck.
I would start by getting an independent contractor who is not involved at all to look at it and tell you if it's right or wrong and what can be done. I'm not sure if they do granite tops but www.naturalstonecareinc.com would be a good place to start, they do marble floors and surely could point you in the right direction.