What happens with Text Replace?
As for the double footnotes, I’m not very familiar with the order in which the content gets filtered and replaced. There are so many filters that take effect: WP’s built-in ones, any shortcodes, and additional plugins such as ones that add sharing buttons. What surprised me when I coded it was that the footnotes were being appended to the end *before* the shortcodes were invoked. I found that unnatural. So there’s probably something I don’t understand about the order of filters.
Without seeing your code, I can probably handle both cases: the shortcode gets processed before and the shortcode gets processed after the original plugin attempts to append the footnotes. So let me try that and update it.