Do you have pictures of the in progress work? I see 3 things immediately. There may be more.

What are the 3 things?

1. Poor materials choice.

2. Poor grout choice.

3. Installer accepting the materials.

4. Choice of tile for s curb when a solid piece of something could have been had.

5. Linear drain location, and installation.

Most of that is poor design. Yet the installer accepted the poor design and chose to go with it anyway, instead of explaining why or walking away.

So contractor came back today more willing to help. Readings on moisture meter were low and pretty even throughout shower which is good. Most of what I can find on forums when the grout gets darker later in random areas it's due to too much water while mixing the grout or the thinset? under the tiles/stone. The latter will just turn new grout dark again. My contractor now realized I used his recommended brand, Mapei, and is not sure if it was a bad batch and wants to do a new thin layer over the existing layer. He is insisting his guys mixed everything correctly. Should I insist he break out a layer of grout to check the thinset?

I'm wondering if it may be oils in spilled shampoo or something of that nature.

Nothing ever spilled in there and it's too random and widespread. I did complain after it was completed that his worker left grout on the pebbles too long and didnt clean it off before he sealed it so they came back to clean it up but I am not sure what they used. Whatever it was did take some color off some of the pebbles which upset me though it didnt change the grout color at that time.

The oddest indicator to me is your first photo, the sliver of "whiteness" on the floor along the wall in the left part of the photo. If that is truly there and not a photo anomaly, I'd not think the problem originates with the grout itself. I'd venture it has to do with something done post-installation; the cleaning, or the sealing.

So many variables, but the overall blotchniness?

Could be the application and use of the product used to clean the grout shmears off of the stone. If the texture of the grout was changed during the cleaning process, the sand papery grout can hold shower residue; soap and shampoo product, etc.

Same with sealer use. If the sealer pooled in some areas versus others, or if the sealer dried on the surface, it can become tacky on a micro-level. You may not feel it, but it can hold dirt off the bottom of your feet, or hold shower residue.

The following two things will typically whiten grout versus causing it to go darker:

Could be efflorescence, but with the linear drain I'm guessing you have a surface applied membrane under the tile. Efflorescence is more common when tiling over an improperly built mud bed or a slab.

Could be latex leaching. Latex leaching can be effected by water usage during the installation, as well as an insufficient grout drying/curing time before the shower was used. Latex leaching will typically lighten a surface, but the latex can hold dirt.

No solid answers from me. Just speculation.

Thank you MongoCT. You are right, there is a layer of redgaurd under the thinset and tile. I don't see a white line on the left of my shower so I think it may be the reflection of the baseboard on the shower door or the sanded caulk. I think you are right that it may be the product they used to clean it. A few pebbles still have some grout on the edges and that grout is darker as well. I'm also curious if they resealed right after cleaning because I never saw them do it later which may have contributed to the issue. We are at week 3 not using our shower and my husband just wants to use it again so we are just going to have them fill the holes and reseal since it is not a water issue. Super annoyed with the whole thing but we are not certain a thin layer of grout would stick and just leave us with a bigger mess and he said he wouldn't warranty the new grout if it didnt work out.