I came across this problem when trying to compile a 60 page academic paper with just over 100 inspector footnotes. Compiling to MSWord would appear to work but while reading through the paper I would discover that some footnotes were doubled and others were missing altogether. I tried compiling to PDF and the doubling stopped but still some footnotes were missing. I converted all inspector notes to inline notes and recompiled. Then I discovered that at least some of the missing footnote markers appeared as this <$FM> in the main text of the paper but there was no corresponding reference in the footnote section. I also noticed that <$FM> as it appeared in the PDF was a link, Hovering over it revealed “scrivcmt:” followed by a massive serial number.
I found nothing describing this same problem on this site (searching for ‘footnote’ in the bug forum) or google. I did come across advice in other instances to try compiling to RTF.
Compiling to RTF seemed to work. The whole bug added several hours of work trying to find a work around and then later manually checking all footnotes for fear some might still be missing. I would like to know how serious the issue is so that I can plan around it on other projects, particularly when I want to compile directly to PDF.
I was using Scrivener Version: 22.214.171.124 (1274136) 64-bit - 28 Apr 2021
This link leads to some screenshots;