Ho Josbarrios,
since the developer didn't update the plugin or responded to any support thready in the last 3 years, I'm guessing, there'll be no answer from the developer's side.
2 quick things, though.
Firstly. I browsed the page you linked and all footnotes seem to be working fine.
Secondly. We wrote a footnotes plugin from scratch to address a lot of issues we had with other footnotes plugins you might as well give that a shot. And Yes, it's compatible with all your current footnotes, as the syntax for marking footnotes is customizable.
https://wordpress.org/plugins/footnotes/