As everyone said, I can't say it any better! But, I'd like to point out one distinction that may help you get the builder to REPLACE the floor.
Since you aren't officially in the home, you can say you paid for a WHOLE floor; not one with patches in it. It would be one thing for you to already be IN the home but you aren't. At that juncture, the 'new home warranty' kicks in (if you have one), and the builder would be allowed to make 'reasonable repairs' (such as a patch.) Again, the fact that you're NOT in the house yet makes a difference in your case.
If you don't have a REal Estate Attorney for closing, now is a good time to get one. This is why I always recommend new/existing home buyers hire one when they begin building a new home (or looking for an 'existing' home.) They are working in your interest. I'm not suggesting you sue the builder. I'm mearly suggesting the Attorney knows how to 'work this type of situation' to your advantage.
As for the bluish stuff, you'll have to ask the builder or a tile pro. My best to ya and hope this helps.