Low-energy argon ion bombardment of graphene on Ir(111) induces atomic-scale defects at the surface. Using a scanning tunneling microscope, the two smallest defects appear as a depression without discernible interior structure suggesting the presence of vacancy sites in the graphene lattice. With an atomic force microscope, however, only one kind can be identified as a vacancy defect with four missing carbon atoms, while the other kind reveals an intact graphene sheet. Spatially resolved spectroscopy of the differential conductance and the measurement of total-force variations as a function of the lateral and vertical probe-defect distance corroborate the different character of the defects. The tendency of the vacancy defect to form a chemical bond with the microscope probe is reflected by the strongest attraction at the vacancy center as well as by hysteresis effects in force traces recorded for tip approach to and retraction from the Pauli repulsion range of vertical distances.