Witn Indesign CC2017 I created an epub, but the footnotes are not working, evean as a popup or at the end of the section. I've tried to export to epun 3 and epub 2.0.1. the same problem: the linf between footnotes is not working. This is the code that inDesign creates when exporting to epub:
" <span class="FNref _idGenCharOverride-4"><span id="footnote-037-backlink"><a class="_idFootnoteLink _idGenColorInherit" href="O_meu_Imaculado_Coração-4.xhtml#footnote-037">1</a></span></span> "
How are you testing the epub?
With iBooks in my iMac, also i've tested with Calibre, with the same results (both apps are updated: the footnote number opens the xml document (O_meu_Imaculado_Coração-4.xhtml) inside the epub, not the footnote.
I have tried to insert footnote in InDesign and exporting it to EPUB 2 and EPUB 3. It is exported fine and looking good with footnotes in place on iBooks..
Can you please confirm if you have any special setting applied to it...
Or you may share your document or Video to show the problem scenario @ firstname.lastname@example.org so that i can investigate further.