One thing I've found is that when 'beautifying' & nbsp; entities get changed to spaces, which is what I don't want.
Edit: Also does it for the 'Fix html' function.
Quite often there's
which will then get ignored rather than having a 'scene-break' empty paragraph.
Also a few instances inside paragraphs where you have deliberate extra spaces or other such occurrences which then get 'reduced' to normal spaces which because of the way they're rendered by readers is now wrong.