From what I've learned converting html to mobi, footnotes need to be properly linked.
Here's an example: html source code
in the book:
ein Leben im Verborgenen geführt haben und in Gräbern ruhen,
die kein Mensch besucht".<a href="#1_1"><sup>1</sup></a>
at the end:
<a name="1_1"></a>
<p width="0" align="left"><sup>1</sup>
George Eliot, <i>Middlemarch</i>,
übers. von Rainer Zerbst,
Stuttgart 1985,
S. 1136.</p>
When you look at the screens attached, you'll see in the text a superscript
1, (kindle shows links underlind), so if you click it, you jump to the note as in screen 2 (and back to the text with the back button)
I found it to be usefull, to end the <a> before, not after the complete footnote, latter causing strange formattings...