If I insert a cite via cut and paste in a note, then the automatic footnote count does not work correctly (see screenshot).
bumped in hopes of getting a response to the post
Unfortunately, the Notes editor doesn't have support for footnotes. When you paste some text in, it's just inserting the text and footnote at that location regardless of whatever else you might already have in the note. I recommend adding a request at https://feedback.faithlife.com/boards/logos-desktop-app for improving the footnote support in the Notes tool.