I would suggest YOU do not not scrub anything and let it be and cure while communicating with the installer. Arm yourself with knowledge and continue to let it cure. Once you yourself touch it it is yours to own and that would give them an OUT. Secondly you cannot remove a sealer unless you first know the brand/type and way it was applied. Something as silly as a dirty rag or compromised sponge could be a major issue when applying sealer to light stone.

Sealing limestone prior to grouting is normal. We set the tile(properly with proper methods materials), let it cure, and then seal lightly with an Impregnator sealer that allows the stone to breathe ( vapor permeable) as it cures this is to assist in grout release/cleanup. On heavily pitted stone I will skip the sealer and match the grout to the stone color so it fills any voids/pitts. So there is never a one fits all scenario with this step and as such cant blame youre installer for sealing as long as its the proper sealer applied to clean dry tile.

In your scenario I am going to lean towards

A. The stone itself is moist and as such is showing its true colors as well as the water from thinset curing....Sandy looking black wash/dots?...common with limestone and more pronounced when moist

B. Thinset & color (doubtful as i can see some white residue but maybe a mix of 2 grey/wht were used?) thinset that is not making full contact with the tiles and not skimmed on underside ( wrong type thinset, bucket grade premixed mastic type, or not mixed properly etc etc etc. . that is still wicking and curing.

C. A sealer issue that is not allowing vapor transmission. Time will help you tell...and again Im looking at one picture and not in youre home close up, with scant information as well.

With all very light color stone I am using only white thinset rated for soft stone. and each tile gets a skim coat on the bottom side, this helps even out color variations as the white cures and has FULL coverage.

Again I suggest you let it cure further and SOAK TEST a New clean piece of the same tile that has not been sealed, let it soak for a nite and then watch it as it dries and compare to youre install.

In my previous post I shared possible indicators and I am not in youre home nor did i watch the install and proper technique/practices. There are a lot of variables that it COULD be and then you are dealing with a very fickle prone to problem material. Limestone.

I will add it is a rookie mistake to tile the whole floor and then eat the cost and do over without confirming door sweep clearance and that is a red flag towards skill and almost always when losing such an amount of money folks will rush thru the second time.. but we all make mistakes. Inquire for pics of how it was set, get documentation of the thinset used and sealer used. And soak a piece as I stated. we call this troubleshooting...

I may ask? how did you source and find this Tile installer? there are a lot of so called tilers out there today, That lack the training and knowledge of professional Tilers....Its the years of practice and failure that make a difference most every time..

Lastly!!!! there is a tilers Installation manual (TCNA 2016 handbook for installation) It has very clear and defined rules for installing stone and can not be debated, from the proper prep work to the install to the sealing......I suggest every homeowner looking to have a tile project done in this new HGTV DIY day and age Buy this manual and use it to cross refrence whats being done when doubts and questions arise it is a safer bet than random Internet advice. - best of luck be patient....