Novel two-dimensional materials have emerged as hybrid structures that combine graphene and hexagonal boron nitride (h-BN) domains. During their growth process, structural defects such as vacancies and change of atoms connectivity are unavoidable. In the present study, we use first-principle calculations to investigate the electronic structure of graphene domains endowed with a single carbon atom vacancy or Stone–Wales defects in h-BN sheets. The results show that both kinds of defects yield localized states within the bandgap. Alongside this change in the bandgap configuration, it occurs a splitting of the spin channels in such a way that electrons with up and down spins populate different energy levels above and below the Fermi level, respectively. Such a spin arrangement is associated to lattice magnetization. Stone–Wales defects solely point to the appearance of new intragap levels. These results demonstrated that vacancies could significantly affect the electronic properties of hybrid graphene/h-BN sheets.