In a companion paper we have presented many products derived from the application of the spectral synthesis code STARLIGHT to datacubes from the CALIFA survey, including 2D maps of stellar population properties and 1D averages in the temporal and spatial dimensions. Our goal here is to assess the uncertainties in these products. Uncertainties associated to noise and spectral shape calibration errors in the data and to the synthesis method were investigated by means of a suite of simulations, perturbing spectra and processing them through our analysis pipelines. The simulations used 1638 CALIFA spectra for NGC 2916, with perturbation amplitudes gauged in terms of the expected errors. Noise and shape-related errors at the level expected for C ALIFA propagate to uncertainties of 0.10-0.15 dex in stellar masses, mean ages, and metallicities. Spectral residuals are of the order of 1% on average, but with systematic features of up to 4% amplitude. We discuss the origin of these features, most of which are present in both in C ALIFA and SDSS spectra.