Some footnotes (near 300) in a book with only one story get bad in this pop-up export setting: punctuation is lost or italic...
The another ones settings: at the end or below the paragraph are ok... The formatting remains unaltered
Also, curiously a couple of item in TOC are displayed in a different colour (!?)
What EPUB reader are you using to view the EPUB 3.0?
Ibook 1.0.1 und Ipad 6.xx
Formatting in footnote text is not supported in pop up footnotes. This is a limitation of iBooks itself.