The physics of vacancies in single layer graphene exhibits a wealth of interesting features. Among them, the existence of zero energy modes, local fractional charge and parity breaking. Recent STM measurements at the vacancy location have confirmed these features. Nonetheless, a surprising and yet unexplained result is the energy shift of these zero modes away from the Fermi energy. We attribute this shift to the interaction of the STM tip with electronic excitations around the vacancies. We have calculated this effect and obtained a good quantitative agreement with the measurements.