Looking at the picture, I have picked out all the problematic glyphs.
It is OK to perform the same operation on the same project in FontForge.
FC version is 15.0.0.3011
CFS.zip (74.2 KB)
We will ensure the next update will come with more improvements related to this, but FontCreator does not like contours that have a tiny overlap, so better make a significant overlap, e.g. more than one unit, or ensure contours do not overlap at all.