The two-dimensional thickness profile of a phase object can be measured by phase microscopy by assuming that the light passes straight through the sample such that the measured phase profile is proportional to the thickness of the sample. However, any non-uniform index structure in a sample bends the straight light path by refraction and diffracts the non-uniform transverse phase structure of the wavefront along the propagation path within a sample. We investigated the consequence of these two effects within a phase object using a split-step beam propagation method that considers beam paths through a 3-lm-diameter bead sample. Our simulation results show that the phase profile of light just after passing through a sample differs significantly from an ideal phase profile. We verified these simulation results by comparing them with experimental data obtained with a Mach-Zehnder interferometer.