Issue 1: Dissolving grout (cracking grout discussed in next comment)

After moving into our remodeled home nine months ago, I asked my son to keep new bathroom sparkling clean. He's done a great job, but now we've discovered that some of the grout on the porcelain tile shower floor seems to be flaking and/or dissolving, especially in the corners. It smudged like wet charcoal when I touched it. It looks like black mold, gross, but it's not. (We live in a dry climate and he keeps the bathroom fan on 24/7.)

The only cleaning product he's used in the shower is Whole Foods 365 Daily Shower cleaner. He followed the directions, which say "Mist all wet surfaces right after your shower and allow to dry." , The product lists only three ingredients: water, cocamidopropyl betaine and citric acid. I have no idea how much citric acid is in the bottle, but could that be the culprit? Could it be dissolving the grout?

If it matters, the grout is Laticrete Permacolor Select in Platinum, which does not require sealing but our GC insisted on it, and the technical expert at Laticrete said it's fine to seal. GC used Miracle Sealants 511 Porous Plus for sealing (I'm now realizing that product is specifically for natural stone and our tile is porcelain...is that a problem?).

I don't think it would be his shampoo or body wash as they are pretty innocuous: Alafia Body Wash and Alafia Shampoo, both made with coconut oil. They are dark brown, though.

Thoughts? Do we need to regrout? We stopped using the Whole Foods shower spray (not using anything now) and that seems to be helping, but wondering what measures to take to remedy the situation.

Thanks!

Photos are shortly after he finished showering, so some of that dark grout is because it's wet.

Flakes of grout (?) just outside the shower door:

One corner, inside the shower.

Smudge after rubbing my fingers across the black grout.

For comparison, here's the master bathroom shower with the same shower floor tile, grout and sealer, which all seem in fine shape. I have not sprayed any cleaner in here yet! I just towel dry the walls after showering and occasionally use a soft brush on the floor grout.

Next up (thanks to millworkman): the issue of the cracking grout where glass meets grout.