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Graphite crystals used to prepare graphene-based heterostructures are generally assumed to be defect free. We report here scanning tunneling microscopy results that show graphite commonly used to prepare graphene devices can contain a significant amount of native defects. Extensive scanning of the surface allows us to determine the concentration of native defects to be 6.6$\times$10$^8$ cm$^{-2}$. We further study the effects of these native defects on the electronic properties of Bernal-stacked bilayer graphene. We observe gate-dependent intravalley scattering and successfully compare our experimental results to T-matrix-based calculations, revealing a clear carrier density dependence in the distribution of the scattering vectors. We also present a technique for evaluating the spatial distribution of short-scale scattering. A theoretical analysis based on the Boltzmann transport equation predicts that the dilute native defects identified here are an important extrinsic source of scattering, ultimately setting the mobility at low temperatures.