Core-level energies are frequently calculated to explain the X-ray photoelectron spectra of metal-organic hybrid interfaces. The current paper describes how such simulations can be flawed when modeling interfaces between physisorbed organic molecules and metals. The problem occurs when applying periodic boundary conditions to correctly describe extended interfaces and simultaneously considering core hole excitations in the framework of a final-state approach to account for screening effects. Since the core hole is generated in every unit cell, an artificial dipole layer is formed. In this work, we study methane on an Al(100) surface as a deliberately chosen model system for hybrid interfaces to evaluate the impact of this computational artifact. We show that changing the supercell size leads to artificial shifts in the calculated core-level energies that can be well beyond 1 eV for small cells. The same applies to atoms at comparably large distances from the substrate, encountered, for example, in extended, upright-standing adsorbate molecules. We also argue that the calculated work function change due to a core-level excitation can serve as an indication for the occurrence of such an artifact and discuss possible remedies for the problem.