In the present work, we explore the effect of hyperthermal species—sputtered particles and backscattered argon (Ar) atoms—on defect generation during sputter-deposition of thin metal films in single-layer-graphene (SLG). Gold (Au), silver (Ag), copper (Cu), and aluminium (Al) targets are magnetron-sputtered at various Ar gas working pressures and respective (Formula presented) thick films are grown on SLG supported on silicon dioxide. The selected target materials: (i) have distinctly different atomic mass numbers (Formula presented) and thereby different propensities to backscatter and transfer energy to Ar+ plasma ions; and (ii) exhibit differences in their surface binding energy, the latter being the quantity that largely determines the most probable energy of the sputtered particles ejected from the target surface. Raman spectroscopy measurements show that decrease of the working (Ar gas) pressure Au and Ag deposition leads to a higher defect density in graphene, while defect formation during Cu and Al deposition is seemingly independent from the working pressure. Moreover, increase of (Formula presented) generally induces more damage in graphene. To understand the origin of defect generation and correlate it with energy and flux of hyperthermal sputtered and backscattered species at various deposition conditions, we use two complementary computational approaches: Molecular Dynamics to model the target sputtering process and Test-particle Monte Carlo simulations to model the gas phase transport of species from the target to the single-layer-graphene substrate. Our analysis shows that defects are primarily caused by energetic backscattered Ar species, such that targets that are less efficient in backscattering Ar+ ions along with relatively high working pressures lead to a minimization of ballistic damage on graphene. The findings presented herein pave the way for developing strategies to achieve defect-free growth of thin metal films on graphene and other van der Waals crystals and thereby enable magnetron sputtering for scalable fabrication of multifunctional metal contacts in two-dimensional-materials-based heterostructure devices.