Second-harmonic generation (SHG) from aperiodic optical superlattices in the regime of pump depletion is investigated, when the influence of typical fabrication errors, which can be introduced by the random fluctuation of the thickness for each domain in the simulation, is considered in accordance with the actual case. It is found that both the SHG conversion efficiencies calculated in the undepleted pump approximation (UPA) and an exact solution decrease when the fluctuation increases; however, the decreasing degree is related to the wavelength of the fundamental wave (FW), and the longer the FW wavelength, the less the decrease in the corresponding conversion efficiency. A relative tolerance with respect to SHG conversion efficiency calculated in the UPA and exact solution is defined as previously [Opt. Express21, 17592 (2013)], in which a typical model based on the relative tolerance curves was proposed to estimate the SHG conversion efficiency. The simulation results show that the relative tolerance curves are basically coincident with the standard curve when the random fluctuation is very small (typically below 1%); however, as the fluctuation increases, the relative tolerance curves exhibit a large deviation from the standard curve, and the deviation is also determined by the wavelength of the FW.