" Is there any way to remedy this without replacing it? "

I would think you would need to speak with the tile manufacturer or dealer for that.

" Should the guy putting them have not seen this and pointed this out?

You would like to think so. Who supplied the tiles? If you supplied them he may not have even looked that close or even assumed you knew what you had purchased.

Have you tried cleaning it?

Unless the tile guy bought the tile, they usually aren't responsible for it and most will install exactly what you purchased, without a second glance for any defects. If you bought it, you should have inspected it.

In the past I have gone through boxes and boxes of hand-made glass tiles, culling the ones that weren't "perfect" and separating ones that had partial "defects" but could be cut and the remaining "perfect" piece could be used. The tile guy would have used every single tile!

See if the tile guy can remove the marks with a "harsher" tile/grout cleaner. If he can't, then you need to decide if you want to start over. Stop the job until you make your decision.

Yes, to trying to clean. As millwork suggested, call the yoke manufacturer.

I'm nit sure the installer would notice it being close up.