These look like "seconds". If got them cheap this is probably why. Did they come packaged?

Some spots look like dried grout to me.

Sophie - this is a high end shower. Contractor works with high end builder. The tile contractor purchased the tiles. I asked to inspect the tiles before they were used, but this did not happen.

Then if that is a 20K shower with $60 a square marble, the GC should have already noticed the stun marks and crevices and be resolving it with his tile technician. Who should have never installed that tile after inspecting it. Those pieces should have been culled on the front end, and additional materials ordered and received if that ate into the cut % too much. The actual resolution will depend on what waterproofing was installed, and the risk of penetrating it by tile removal. But that is why you hired a top tier GC to oversee the work. Let him earn his 25% and chew butt like he is supposed to be doing. It is only if he doesn't resolve the issue that you raise your disappointment.

They shouldn't have used sanded grout or used that size of a grout spacing on marble tile in a shower installation. Actually to be fair the grout spacing is right on the edge of too big but in a shower you usually tend to go as small as possible especially with marble as it allows a tight accurate grout spacing.

Hard to tell in pic but is that actually in the tile or grout? Natural stone will have defects and there is always an odd looking tile or two unless a very high end installation.

The smaller marks are no big deal it is that larger one that the installer should have caught.

Try scraping off with a fingernail.

Grind out the stun marks, fill them and polish.