Rub a tiny bit with hydrogen peroxide or lemon juice, distilled white vinegar. Let it dry and see if it will bleach it or lighten it.

It looks like this happened before install because the stain does not cross the grout line onto the next tile.

What did the tile worker use to clean and prep the tile?

Did the tile installation company have any feedback on the staining (I know you said their worker did not).

Consider holding off on grouting until this issue is sorted out.

Not an expert here:

It doesn't look like staining to me. I have limestone floors (gray though) for more than 10 years. They are impervious to any staining at all, with hard, hard use and no preventive care at all.

Your floors are gorgeous, I love them, and in your photos, you show only 3 tiles out of the room with the "staining". It doesn't look like staining to me... it looks like natural variance, but again I'm not an expert.

The photo of the floor as a whole looks fabulous, and the stains do not make an impression in the overall appearance.

I suggest you replace those 3 tiles and move on.

Could be just moisture from the install that will dry out since it needs to be dry underneath before grouting anyway. Were all the tile boxes opened and sorted to make sure no odd ones ? Fo me it is not a huge deal I know tyou see it but I promise no one else will and how many of those will not even be visible when you are done ?

Could also be naturally occuring iron deposits showing themselves. Not unusual in real stone products made by Mother Nature.

Thanks to you all for the comments. The discoloration was not on the tiles when they were laid last night. I’m waiting to hear back from the installer. I love the overall look

Looks like naturally occurring iron deposits to me- that happened on some of my 2 inch marble hex tile sold as Carrara by Akdo Tile- luckily noticed before grouting- and it turned the marble was from China, not Carrara. Neither the sales person at the (rather upscale) tile store nor the person I initially spoke to at the tile company were aware this was not actually Italian marble. Luckily the tiles with orange stains were easily swapped out, and two+ years later there haven’t been any more stains. Whew.

Iron deposits will rust when exposed to moisture. Never use any acidic substance on limestone. Including rust removers. It will dissolve it.

China at. From everything I have read it it does look like iron deposits. But they weren’t there when he came to clean the tiles today but showed up afterwards. I’m wondering if the water had a high iron content that they used.

Iron content water only showes up gradually, as a buildup. Iron inside the stone usually shows up at setting, when the moisture in the thinset and oxygen reach the cut surface simultaneously.

Amy that makes sense since the tiles were laid on the thinset yesterday and just showed up when he put water on them today

Swap those out, wait to grout to see if any other iron spots show up. Then seal before and after grouting.

have limestone floors (gray though) for more than 10 years. They are impervious to any staining at all,

Limestone is porous; it is the very opposite of impervious. Only sealant can reduce this.

I 100% agree that those need to be swapped out, regardless of how they occurred, and then wait to seal.