Measurement of picometer-scale atomic displacements by aberration-corrected STEM has become invaluable in the study of crystalline materials, where it can elucidate ordering mechanisms and local heterogeneities. HAADF-STEM imaging, often used for such measurements due to its atomic number contrast, is generally considered insensitive to light atoms such as oxygen. Light atoms, however, still affect the propagation of the electron beam in the sample and, therefore, the collected signal. Here, we demonstrate experimentally and through simulations that cation sites in distorted perovskites can appear to be displaced by several picometers from their true positions in shared cation− anion columns. The effect can be decreased through careful choice of sample thickness and beam voltage or can be entirely avoided if the experiment allows reorientation of the crystal along a more favorable zone axis. Therefore, it is crucial to consider the possible effects of light atoms and crystal symmetry and orientation when measuring atomic positions.