Work with copies!

Your footnotes should be formatted using the Footnote Text style.
Your footnote numbers should be formatted using the Footnote Reference style.
Your endnotes should be formatted using the Endnote Text style.
Your endnote letter/numbers should be formatted using the Endnote Reference style.

You body text, etc should have a different style. It sounds like everything may be formatted using the normal style.
Importance of Styles in Word

Could you upload a couple of pages with the problem (and no confidential or proprietary information)?
How to attach a file in this forum.