Last modified: 2013-10-04 00:19:23 UTC
VisualEditor needs to preserve adjacent (even if identical) and additive elements that it internally treats as annotations. Right now it often removes nested annotations (bug 49755) or merges adjacent annotations (bug 49873, http://en.wikipedia.org/w/index.php?title=Bose%E2%80%93Einstein_condensate&diff=prev&oldid=562481552). Both will lead to a DOM diff and thus likely to a dirty wikitext diff. Note that this only applies to existing content- merging identical annotations in new content is fine.
Also, don't cut annotations. This is what I suspect happened here: http://en.wikipedia.org/w/index.php?title=List_of_Mystery_Science_Theater_3000_episodes&diff=prev&oldid=562488147
This has been fixed for some time in the DM. Marking as such.