Numerical simulation models that are used to investigate the near-Earth space plasma environment require sophisticated methods and algorithms as well as high computational power. Vlasiator 5.0 is a hybrid-Vlasov plasma simulation code that is able to perform 6D (3D in ordinary space and 3D in velocity space) simulations using adaptive mesh refinement (AMR). In this work, we describe a side effect of using AMR in Vlasiator 5.0: the heterologous grid approach creates discontinuities due to the different grid resolution levels. These discontinuities cause spurious oscillations in the electromagnetic fields that alter the global results. We present and test a spatial filtering operator for alleviating this artifact without significantly increasing the computational overhead. We demonstrate the operator's use case in large 6D AMR simulations and evaluate its performance with different implementations.