Images stacked by using 'Do Stack' often have erronious pixels or areas in them, there are many ways to edit these out. You could also use some of these to 'seed' a difficult area with some pixels before stacking, just Fix these first.
The simplest method is to 'Delete Pixels' or 'Delete Rectangles' or to use a seeded delete ('Shift+C' while pointing at the starting pixel). These methods can be modified by switching to Plane Mode first, thus you could delete the contribution from one Frame in a rectangular area by deleting a rectangle while in Plane Mode. Combined with a view of the 'Depthmap' you can use a seed clear operation to delete all contiguous pixels from one level. After deleting some pixels you will be left with one or more holes in the Picture, fill these with 'Fill Gaps' or 'Paste Active Under' etc.
Another easy method is to paint over an offending area with individual pixels or a seeded fill or overwrite with a rectangle. The trouble with this method is that the joins may not be so attractive as with the last method.
Another more subtle method is to smoothe the depthmap, or to remove islands, both of these methods are used by the default Do Stack Macro.