Looks like moisture to me. No way to know without ripping the tiles out.

What material is the new tile? Could it be moisture? Some types of tile can absorb a lot of water during installation. I had some that did although the darker spots were on the edges.

Close up

Hmm. Maybe the tile-on-tile installation is causing some sort of moisture issue. Is there a reason the old tile wasn't pulled up before the new tile went down?

Or, was sealer used on the tile after installation? Those are the only two explanations I can come up with; perhaps our resident tile experts/installer would have more to add.

They are procelain tiles

will moisture stain go away or is it permanent?

will more come up like I said every day more appears!

should porcelain tiles even absorb like this?

@Sabrina Alfin Interiors It was easier not to pull up the old tiles and we were told it was ok.

we did another room next to it same way but no issues with that room ..

No sealer was used on the tile after installation, just grouting

Normally they don't, but I've never seen tiles installed on top of tiles. I'd bet money that has something to do with it.

@socialgal_gw did it go away eventually or stay as is?

Down here in Florida, they lay new tiles over old tiles all the time with no issues.

Were the tiles "seconds"?

Is the mortar from one room to the other different?

At least one tile will have to be removed to see what is happening below.

Our moisture issue eventually went away. Our tiles were not porcelain, they were ceramic. They absorbed water almost as well as a sponge. If I put a drop on the back it just soaked right in.

We had troubles at two stages. One was during the wet sawing of the tiles. The cut edges absorbed lots of water. They were installed and the dark areas went away in a few days. The second problem was water getting in (it was a shower) through the joint between the wall and the floor. Caulking the joint took care of that problem, but it took a lot longer to dry out and go away, perhaps weeks?