Transparent conducting oxides, like indium tin oxide, enable lateral charge carrier transport in silicon heterojunction solar cells. However, their deposition can damage the passivation quality in the solar cell. This damage during the sputter deposition is a complex issue that has not been fully understood, particularly in various silicon‐based materials like amorphous silicon, polycrystalline silicon, or nanocrystalline silicon carbide. The degradation in passivation quality observed in, for example, amorphous silicon is not only explainable by UV light degradation. This study explores the origin of this degradation based on the example of hydrogenated nanocrystalline silicon carbide by combining simulations with experimental analyses. It delves into potential sources of damage during the sputtering process and determines that neither primary nor secondary effects from plasma luminescence or electron bombardment are likely contributors to the damage. Similarly, the implantation of ions, as well as the creation of vacancies and ionization of lattice atoms, are also considered improbable causes. It is, however, proposed that the transfer of energy to the crystalline silicon interface via phonons can factor into the degradation of the passivation quality. This transfer might be a plausible explanation for the damage observed in the passivation layers during the sputtering process.