GOMOS is a stellar occultation instrument onboard ENVISAT. It has already measured several hundreds of thousands occultations since March 2002. In some circumstances, the obliqueness of the star setting causes the remote sounding of possible horizontal turbulence that cannot be adequately corrected by using the fast photometer signals, leading to the presence of residual scintillation in the atmospheric transmittance. We investigate the mechanism that produces this spurious signal that may cause the retrieval of wavy constituent profiles. A special algorithm of vertical autoregressive smoothing (VAS) is proposed that takes into account the physical correlation between adjacent measurements at different tangent altitudes. A regularization parameter of the method may be optimized on basis of the minimal correlation between the residuals as prescribed by the Durbin-Watson statistics. The improvements obtained in the retrieval of both O3 and NO2 number density profiles is presented and discussed with respect to the results of the official data processing model.