InDesign'dan ePub'a

Footnotes in EPUB are always a little quirky, and the recent structural change hasn't helped. Two things to try —

First, what EPUB reader are you using? They vary in both quality and fidelity of presentation. Have you checked your book in the fairly standard Calibre Reader and Thorium Reader? Kindle Previewer is a good check tool even though it's converting the format, as well. You may find that your footnotes and other formattting are fine in these readers, and that's about all you can do. (You can optimize versions for variant readers such as Apple's but that's a separate workflow if you plan to release the book to a general EPUB market.)

Also, try the different export options. Between how export handles them and how each reader handles its own options, you will probably see some variation in how the notes are presented, whether the numbers or markers are reliable, etc.

My solution is to bypass all the wonky, clever link and pop-up features, which are too dependent on too many export and reader issues, and simply embed the notes inline, as a paragraph formatted small and to the side. It's completely hassle-free and IMHO does not disrupt the flow of the book and text any more than notes do in a printed book:

A recent update to InDesign means that the footnotes are now exported as lists, which is the semantically correct way to make notes. The EPUB export it creating a small piece of CSS that designates those lists to have no numbering. If you are comfortable editing the CSS, you could look for list-style-type:none; and delete it.