  In the HERAPDF2.0 PDF analysis it was noted that the fit $\chi^2$ worsens
significantly at low $Q^2$ for both NLO and NNLO fits. The turn over of the
reduced cross section at low-$x$ and low $Q^2$ due to the contribution of the
longitudinal cross section $F_L$ is also not very well described. In this paper
the prediction for $F_L$ is highlighted and the corresponding extraction of
$F_2$ from the data is further investigated, showing discrepancies with
description of HERAPDF2.0 at low $x$ and $Q^2$. The effect of adding a simple
higher twist term of the form ~$F_L*A/Q^2$ to the description of $F_L$ is
investigated. This results in a significantly better description of the reduced
cross-sections, $F_2$ and $F_L$ at low $x$, $Q^2$ and a significantly lower
$\chi^2$ for the NNLO fit as compared to the NLO fit. This is not the case if
the higher twist term is added to $F_2$
