It appears that it is only when the footnote is at the end of the page's text but I'm not sure.
This is a classic footnote layout problem. When the indicator is on the last line, including the footnote would remove the last line, pushing the footnote reference to the next page. Then you wouldn't want the footnote on the first page, which would again create space to pull the indicator back to the first page. Begin infinite loop....
In traditional paper typesetting, these problems are "fixed by hand." Things are pushed around to make the problem go away; we don't have that option here (without a much more expensive multi-pass layout system), so sometimes this happens. We don't plan to address it for a very long time, until performance (and available coding time) is available to write a mutli-pass layout system that does things like subtly adjust margins, change line spacing, add space between paragraphs, etc. to resolve this and other -- widows, orphans, rivers, sequential line hyphenation, etc. -- problems
I understand and agree with your priority on this ... but I'm in the role of tester now so I put it on the list.[H]