Losing formatting and punctuation in some footnotes : epub 3.0/ pop-up options

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 (!?)

Hi Camilo,
Formatting in footnote text is not supported in pop up footnotes. This is a limitation of iBooks itself.
Regards,
Pooja

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