On the limitations of statistical absorption studies with the Sloan Digital Sky Surveys I--III.

We investigate the limitations of statistical absorption measurements with the SDSS optical spectroscopic surveys. We show that changes in the data reduction strategy throughout different data releases have led to a better accuracy at long wavelengths, in particular for sky line subtraction, but a degradation at short wavelengths with the emergence of systematic spectral features with an amplitude of about one percent. We show that these features originate from inaccuracy in the fitting of modeled F-star spectra used for flux calibration. The best-fit models for those stars are found to systematically over-estimate the strength of metal lines and under-estimate that of Lithium. We also identify the existence of artifacts due to masking and interpolation procedures at the wavelengths of the hydrogen Balmer series leading to the existence of artificial Balmer $\alpha$ absorption in all SDSS optical spectra. All these effects occur in the rest-frame of the standard stars and therefore present Galactic longitude variations due to the rotation of the Galaxy. We demonstrate that the detection of certain weak absorption lines reported in the literature are solely due to calibration effects. Finally, we discuss new strategies to mitigate these issues.