I would be too, it's an annoying situation. You could probably try disabling this plugin for a few days to see if the crashes go away. As you mentioned, there isn't much useful information yet, so this might be a bit of a waiting game.
I think if I understand you correctly, the trouble you're facing is that you're losing footnote highlighting/formatting when switching to the rich text editor? If thats right, then there isn't much I can do to help you here. The purpose of this plugin is to extend the functionality of the Markdown/plain text editor, it doesn't touch the rich text editor at all.
You could perhaps suggest a plugin.
There is a document about the limitations of the rich text editor that you might find useful.