Tough to say, some of those look natural, some may not be. Typically marble tile is sealed before and then again after install from what I know.

I have no idea from the pics but usually any natural stone has marks and bits of different tones . I am trying to figure out what the tile was installed before the major construction was done. Ususally the floor would be covered with a tougher material than paper too. Yes it should have been sealed prior to install even but I guess you need to now pick your battles the time to ask this question was when they were being installed.

You didn't inspect the material before installation? And sort out the culls from the acceptable ones? There's always variations in natural stone. Even Thassos has some inclusions. Which is why you buy the highest grade possible with it. Not Floor and Decor or box store material.

The stone should offgas the thinset and grout for a couple of weeks before being sealed. On a production schedule, that delay isn't going to be built in, to let it all sit idle while that happens. The floors will be covered, and the rest of the work will proceed.

If the protection was inadequate, you can have your builder try a poultice. But that can make it worse sometimes, if is a stain and not an inclusion.

Sealing won't prevent abrasions, or etches, or even stains. It just buys you a bit of time.

What your floors look like is what real life living looks like with marble floors.

Thassos white has few inclusions, bit since it's stone, it will have some. Here is a close-up of a typical Thassos white tile. The darker streak is an inclusion. Some are much darker than this image shows.

Of course, the tile in the showroom is almost always pure white. The fact that some inclusion will be present is typically only revealed in the fine print on the box.

The marks in your photos look like typical inclusions to me. If your contractor has thoroughly cleaned the tile, any remaining "marks" are probably native to the stone.

It is really hard when a new install of anything does not look perfect. And, it is smart that you are asking. But, these probably seem very obvious to you now and won't at all in your daily life once you have moved everything in and aren't focusing on the floors. Plus, you will make all of your own marks on this very unforgiving floor surface and won't be able to distinguish those from the ones that are there now.

DeWayne, No we didnt inspect every tile before. That was just inexperience on our part.

Our tile came from Daltile. The builder did have someone come back through and try and buff it afterwards and it actually looks worse than before they tried.

As you can see it was not covered for a lot of the time during construction. Once the paper was ripped it wasnt really replaced.

We did our research and understand marble is a natural porous stone and it will get stained and such. However, that was expected to happen after we moved in and lived in it. Not before we have even closed.