Large Eddy Simulation (LES) of turbulence in complex geometries is often conducted using discretizations with highly inhomogeneous resolution. The issues associated with resolution inhomogeneity are related to the noncommutativity of the filtering and differentiation operators, often referred to as the commutation error. While the commutation error is well recognized, it is often ignored in practice. Moreover, the commutation error related to the implicit filter (i.e., projection onto the underlying discretization) has not been well investigated. Most of the previous work concerning the commutation error has only applied to smooth convolution filters or has only addressed the additional commutation error that arises from applying explicit filters on top of the implicit filter. Modeling of the implicit commutation error that arises from the noncommutativity between numerical projection and differentiation is crucial for correcting errors induced by resolution inhomogeneity that arise in practical LES settings. Here, we investigate how the implicit commutation error manifests in simulation and demonstrate its impact on the convection of a packet of homogeneous isotropic turbulence through an inhomogeneous grid. A connection is made between the implicit commutation error and the propagation properties of the underlying numerics. A model is proposed for the correction of these issues in the case considered here, which highlights important characteristics of commutation models for LES and the importance of considering numerical properties during the formulation of subgrid stress models in general. Several insights are discussed that could also be applied to other issues in LES, such as discretization error.