Thanks for posting on the forum.
To troubleshoot, I’ll really need to see the document.
First, though, it’s worth checking that the GREP expressions that you’ve created (or that were created automatically by Footwork) are not finding some extra “footnotes” by mistake. However, judging by the screenshot you sent previously, that doesn’t seem to be the case.
So, I’ll need to have the document to check what’s going on. Are you able to send it to me?