Oy.. Tristan you said this is a kitchen countertop -------do you know of any such cleaner or product you have there like Joseph suggested? I hope that's not the case.

Not that I’m aware of at all. The only acidic thing that could’ve gotten on there is vinegar.

Perhaps your slab had been dyed. https://www.stoneworld.com/articles/84930-fading-issues-with-black-granite

Is the surface etched or feel roughed up at the stained portions now?

What is the countertop material?

Surface doesn’t feel etched or roughed up - just a weird discolored. It’s granite of some sort.

If you scroll to the bottom of this thread you will see a photo that is similar to yours. Hopefully you can get someone local to take a look at it. I would start with the contractor or fabricator if you happen to know who they are.

https://www.countertopspecialty.com/granite-counter-top-care.html

Someone had a clog and didn’t know how to use a simple drain auger. Instead they used nasty chemical drain cleaner, and splashed it.

The counter is done for. Replacement time. But, you might clean with acetone and then try a permanent leather dye on those spots first, to disguise it. That might buy you some time before the inevitable. Or it might be splotchy, and you have to try to dye the whole thing. But you have nothing to lose.

Since the OP reports that the surface doesn't feel etched or rough, is it possible that these spots are just natural inclusions?

No. They are acid etches. The acid eats the color and leaves the gloss.