The appearance of 3-D vortex structures makes the flow generated by the uniform oscillating pressure gradient over a wavy wall much more complex than the simulated one, and may completely obscure the scenario of transition to chaos observed. As such, a code is used to analyze the characteristics of the oscillatory flow over a wavy wall taking into account 3-D effects and to clarify the process leading the flow from a periodic behavior to an aperiodic one. Moreover, small imperfections are added to the wall profile considered by Blondeaux and Vittori to investigate whether the perturbations induced by these imperfections are amplified by the hydrodynamic system thus changing flow characteristics even for weak 2-D flows.