A family of Microsoft word processing software products for creating web, email, and print documents.
Your description suggests the footnotes themselves have the Footnote Reference Style applied; they should only have the Footnote Text Style (or another suitable Style) applied. The following macro will re-format all footnotes with the Footnote Text Style, leaving the references superscripted (and in the Footnote Reference Style).
Sub RepairFootnoteFormats()
Application.ScreenUpdating = False
Dim FtNt As Footnote
With ActiveDocument
.Styles("Footnote Text").Font.Superscript = False
.Styles("Footnote Reference").Font.Superscript = True
For Each FtNt In .Footnotes
FtNt.Range.Style = "Footnote Text"
FtNt.Range.Font.Superscript = False
FtNt.Reference.Style = "Footnote Reference"
Next
End With
Application.ScreenUpdating = True
End Sub
For PC macro installation & usage instructions, see: http://www.gmayor.com/installing_macro.htm
For Mac macro installation & usage instructions, see: http://word.mvps.org/Mac/InstallMacro.html
Do be aware that any intended superscripting in the footnotes will have to be re-done after running the macro.