One flaw in the Kindle display system is that it can’t deal properly with footnotes. It can’t shove text up on a page to make room at the bottom like a word processor does. In my InDesign Kindle export plugin, you get three other choices:
Footnotes at the end of a paragraph.
Footnotes at the end of a chapter,
Footnotes at the end of the book.
The good news is that a footnote in Kindle is “clickable,” so that if you click on the footnote callout it takes you to wherever the footnote is. Hit “back” to get back to the story.
I have a load of Terry Pratchett books on my Kindle (he’s one reason I like to use footnotes in fiction). Oddly, they’ve used all three methods of locating footnotes, depending on the book. No consistency in presentation, but that’s hardly new in Kindle versions of existing books (that’s a whole post on its own). The one I found easiest to read, without breaking up the story, was the “end of book option,” so that’s where I’ll put them too.