I couldn't see any footnote numbers on the site linked in your earlier comment. Your tooltips appear to be associated with a different plugin (Explanatory Dictionary?).
Not sure what the problem is, but here's a quick checklist:
- Confirm that you've placed the Side Matter widget in your sidebar.
- Make sure any needed page/post types (i.e. home page, single post, etc.) are checked on the Side Matter options menu under Settings > Reading.
- Enclose any note text on your page with the
[ref]Note text here[/ref].
- If your site still isn't working, the issue is likely caused by your theme or another plugin.