A broad variety of defects has been observed in two-dimensional materials. Many of these defects can be created by top-down methods such as electron irradiation or chemical etching, while a few of them are created along bottom-up processes, in particular during the growth of the material, in which case avoiding their formation can be challenging. This occurs e.g. with dislocations, Stone-Wales defects, or atomic vacancies in graphene. Here we address a defect that has been observed repeatedly since 2007 in epitaxial graphene on metal surfaces like Ru(0001) and Re(0001), but whose nature has remained elusive thus far. This defect has the appearance of a vacant hill in the periodically nanorippled topography of graphene, which comes together with a moiré pattern. Based on atomistic simulations and scanning tunneling microscopy/spectroscopy measurements, we argue that such defects are topological in nature and that their core is a stacking fault patch, either in graphene, surrounded by loops of non-hexagonal carbon rings, or in the underlying metal. We discuss the possible origin of these defects in relation with recent reports of metastable polycyclic carbon molecules forming upon graphene growth. Like other defects, the vacant hills may be considered as deleterious in the perspective of producing high quality graphene. However, provided they can be organized in graphene, they might allow novel optical, spin, or electronic properties to be engineered.