The problem has not completely be solved, because it remains impossible to have footnotes inside markup that is not inside the main text flow (this also concerns graphics, mathematical constructs such as fractions, ornaments, etc.).

But the footnote facility has now been greyed out for the most annoying cases.  Instead you should use the notes from the Link menu (see The Jolly Writer, pages 137-138).

In the future, we might design a better way to detect whether we are in the main flow.  If not, then we might insert a note container for the innermost parent that is in the main flow. But this is less urgent, so I put it on the wish list.