Something does not add up. Usually an undermount sink is sealed by a bead of caulk on the sink rim which seals against the underside of the granite. Only a very tiny bead of caulking would actually even be visible.
As far as caulking that joint now, 100% silicone should be the material of choice. It does not stain granite. Whatever they are using is either not compatible with the granite, or with water, or they are applying it to a wet joint.