What makes me think it is natural is the different crystaline structure right there. Do you have a photo of the counter without that mark? You can have such things in natural stone.

Are we talking about the circular area?

It looks like part of the stone to me.

If you truly believe that it is not a part of the stone have an expert look at it, if only to know for yourself.

My did is a geologist and he told me that often what is commercially called granite is not actually granite to a geologist. My multi-color red granite is actually gneiss. It has little garnets and stuff in it. To me it is cool and fun.

It looks like part of the stone to me. I can see why that would look out of the ordinary but its similar to finding a knot in wood. Its just a natural varient in the stone.

I think this video might help you