If the dark current subtraction was not correct, thus if an incorrect offset correction has been applied, the respcal step (which is a gain correction) can introduce incorrect shapes of the continuum or false features.
A good way to check if the dark current subtraction has been done properly, is overplotting the spectrum after respcal with the RSRF and checking if you see residus of the small features in the RSRF.
Examples are given in figures 1 and 2.
Figure 1: The dark subtraction has been done properly: if we overplot the
RSRF (solid line below the spectrum),
we see no agreement between the features
in the RSRF and the spectrum. The solid line through the datapoints of the
spectrum is a model atmosphere.
Figure 2: The dark subtraction has not been done properly: if we
overplot the RSRF (solid line through the spectrum),
we see that the features in the
spectrum are not real. Also the slope of the spectrum is not real (compare
to the model atmosphere printed above the spectrum) Flatfielding the AAR
might help to decrease the scatter between the different detectors, but it
will never correct for the real problem.