Unfortunately I think it is just the nature of marble. I was going to suggest the baking soda water paste - did you leave it on there for a bit?

Marble etches naturally when it comes in contact with most liquids etc. I really do not think it's a matter or sealing/improper install - but I would call the fabricator and see if they have another suggestion.

I left the baking soda paste on for 5 hours. Not long enough? I’m under the assumption my contractor messed up and never actually applied sealer.

From a quick web search:

Etch marks are dull spots from acidic or chemical corrosion. Since an etch mark is clear or whitish in color it is often called a "water stain" fueling the myth. It is not caused by water, nothing has absorbed into the marble, nothing is on the marble and it is not a true stain.

Etching is physical damage to the marble like a burn. Marble polishing is required to repair an etch mark, but it's a simple DIY process using the Etch Remover / Marble Polisher product.

To help avoid etching only use products safe for marble maintenance and minimize contact with acidic foods, drinks and personal products.

And one last piece of the puzzle... sealing will not prevent marble etching.

Yes, sealers help prevent absorption and staining, but cannot stop the physical surface damage that occurs with etching.

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I'm not sure if the etch remover products that mention work on both polished and honed marble. But would be worth checking out. ?