If that's the case, Moon+ and Calibre don't seem to be
supporting the epub 3 spec as directly as Apple does,
though—according to the
Structural Semantics Vocabulary for epub 3,
footnotes should be contained in tags marked with
epub:type=footnote" and then
epub:type="noteref"s for the
superscripted symbols in the body.
This is some body text with a footnote reference. 1
Note that this behavior is purely optional—epub 3 has the
ability for publishers to tell the reading system what kind of
content a particular section is, and it is up to the reading
systems to decide what they want to do with that
EDIT: Based on your comment, it sounds like since there is
hack-y going on or the reading systems you're using are looking for
particular classes and associating special behavior with them.
this blog post, I'm guessing the former—it
sounds like you can include the correct namespacing in an epub 2
file to allow
epub:type to work, and change the
tag to a
display: none on its
CSS to get this to work in iBooks, which Moon+ and
Calibre might be copying.