First, we addressed how to identify vibrational modes of the QM subsystem that include relative motions between the QM and MM subsystems and can be characterized as pseudotranslation and pseudo-rotation. This revealed that up to nine of the lowest-frequency modes were affected for the systems where the QM subsystem only included the solute. For the system with an expanded QM subsystem, thirteen normal modes were affected, indicating that larger and more flexible QM subsystems are more prone to experiencing pseudo-translational and pseudo-rotational contributions in their normal modes. This suggests that as the QM subsystem is expanded to include more solvent molecules, the coupling between the QM and MM subsystems becomes more pronounced, leading to additional modes being influenced by these mixed motions. As a result, careful attention must be paid to properly identifying and removing these pseudo-translational and pseudo-rotational modes to avoid misinterpreting the vibrational spectrum. We also investigated the impact of removing the pseudo-translational and pseudo-rotational contributions by projecting out translation and rotation. This will remove the pseudo-translational and pseudo-rotational contributions, but since the modes are usually mixed modes, any internal motion of the affected modes is redistributed to other modes. Thus, some normal modes can be adversely affected by the projection. Instead of projecting out translation and rotation, the normal modes with substantial pseudo-translational and pseudo-rotational contributions should be removed.