The granite panels above our fireplace have developed several dark circles near the corners of each panel. The granite is only three months old. Should I call the contractor and have them replaced?

I would call the contractor, but it may not be necessary to replace the panels. These dark circles may be the result of moisture bleeding from the setting mortar. It is common for panels to be installed by spotting the backs of the panels with setting material. It may be that this setting material has not thoroughly dried, and you are seeing the moisture bleeding through. To be sure, have the contractor take moisture readings. Moisture in granite can take months to dry out completely.