That is really surprising. Have you done a water test on it? Did you leave the mat on overnight?

I have not had this issue with granite, but I did remove a rust mark from a cast iron skillet using vinegar and baking soda (nothing else worked - I tried everything), so you could try that.

ETA: I use a silicone pastry mat (OXO) under my cutting boards daily, and don't always put it away, and never had marks.

I did leave the clear vinyl mat on overnight. i was told to never use vinegar on this coun becbecause fantasy brown is actually dolomite and would etch. i just had it polished and sealed last week.

I wonder if the something in the mat reacted with the sealer.

You've etched the top. Get a pro out to remove them please. FB etches when you look at it.