When I have italicized body text with punctuation, and a footnote applied, the compiled reference numerals are doubled. One is placed inside the punctuation and the other outside.
For example John, in the text (all italics, and with attached footnote) appears compiled as John45,46 (with the numerals superscripted. Both numerals link to the same footnote information.
Windows 8.1, Scrivener 3.1.3.0, Kindle Previewer 3.70.1