I'll have one last crack at it
When you tap a link that points to footnotes.xhtml, you get a pop-up window on the screen.
The text that's grabbed by the Kindle for the pop-up is from the footnotes file... from link to link. Using the "regular" footnotes link and back-linking (that I probably learned off here!) works just fine.
But if you add headings to the footnotes folder, the pop-up blindly grabs them too, if they appear between links. If you want to exclude the headings, then you have to add the empty <a> links to fool the software into hiding the "overlap" of the heading in the pop-up window.
from the footnotes.xhtml...
<p>
<a href="../Text/ch01.xhtml#ft01" id="fn01">^</a> My first footnote</p>
<p><a href="../Text/ch01.xhtml#ft02" id="fn02">^</a> The second footnote</p>
<p>*Chapter 2's Footnotes</p>
<p><a href="../Text/ch02.xhtml#ft03" id="fn03">^</a> Chp2's footie</p>
So for the first footnote, it'll grab all the text in the orange. Fine.
For the second, all the red text... including the heading you don't want. Adding the ghost link at * forces the pop-up window to break there, and the chapter 2's first footnote then starts over at <a id="fn03">...
Better explanation?