Well, I’m not sure if you just didn’t mention it. But when I test this, it doesn’t make it superscripted until after you have a corresponding footnote. As soon as I add the footnote, it superscripts for me.
If you do have a foot note, and just didn’t mention it, could you show a screenshot or something? And test it in the Help vault with no plugins, just in case.
yadi yada yada [^1].
[^1]:Testing this out.