A number followed by a period is not a standard Word footnote reference style, so the period after is most likely added later and is not actually part of the footnote reference.
Or maybe the OP isn't referring to a footnote reference style, but to the document's punctuation...
The following macro ensures all Footnote & Endnote references are placed afterany applicable adjacent punctuation marks. Any preceding space characters are also deleted.
Sub FootnoteEndnoteFix()
Dim FtNt As Footnote, EndNt As Endnote, Rng As Range
With ActiveDocument
For Each FtNt In .Footnotes
Set Rng = FtNt.Reference
With Rng
'Eliminate any spaces before the footnote
While .Characters.First.Previous.Text = " "
.Characters.First.Previous.Text = ""
Wend
'Swap the footnote/punctuation, as applicable
Select Case .Characters.Last.Next
Case ".", ",", "!", "?", ":", ";"
.InsertBefore .Characters.Last.Next
.Characters.Last.Next.Delete
End Select
End With
Next
For Each EndNt In .Endnotes
Set Rng = EndNt.Reference
With Rng
'Eliminate any spaces before the endnote
While .Characters.First.Previous.Text = " "
.Characters.First.Previous.Text = ""
Wend
'Swap the endnote/punctuation, as applicable
Select Case .Characters.Last.Next
Case ".", ",", "!", "?", ":", ";"
.InsertBefore .Characters.Last.Next
.Characters.Last.Next.Delete
End Select
End With
Next
End With
End Sub
To ensure Footnote & Endnote references are placed before any applicable adjacent punctuation marks, change:
Select Case .Characters.Last.Next
Case ".", ",", "!", "?", ";"
.InsertBefore .Characters.Last.Next
.Characters.Last.Next.Delete
End Select
to:
Select Case .Characters.First.Previous
Case ".", ",", "!", "?", ";"
.InsertAfter .Characters.First.Previous
.Characters.First.Previous.Text = ""
.Characters.Last.Font.Superscript = False
End Select