Basically three approaches to fixing a step.
Best, and least labor-intensive -- though not always doable -- is to carefully 'recrack' the seam, then clamp (with rubber-bands, wedges, clamps, or whatever will work) again so the seam is level, and reapply adhesive.
Both the other two choices are less advisable, but may be necessary in some cases. You've either got to:
a) fill the low side with putty, epoxy, or scrap, until it's level with the higher side; or
b) plane/sand down the high side to match the lower.
Both are likely to involve messy structural recontouring -- in addition to whatever panel lines and detail needs to be restored -- and may also throw subsequent assembly steps out of alignment.
Much better to try to deal with such mismatches during preliminary assembly. The use of shims, internal struts from sprue scrap, or the like to bring the part sides level can solve such problems much more easily beforehand than after the fact. ALWAYS test-fit...at least twice.