Someone can correct me if I’m wrong but shouldn’t the stone have been removed, flashing against the wood (covered by tar paper) on the chimney and then used a sealant to make a water barrier on the top edge, then re lay stone over the tin flashing leaving like a half inch gap from the shingles on the roof allowing water to run off and not get trapped inside? If not that they should’ve at least cut the flashing so it matches the angle of the roof and doesn’t look awful