In the Insert | Footnote dialog, double check that "custom mark" is not
selected.  Also make sure Number Format is set to 1, 2, 3.  There is an
option that ticks through various symbols.

To get to Number Format in Word 2001 and earlier, click on Options in the
Insert | Footnote dialog.  In 2002 and later, I think the option is apparent
in the Insert | Reference | Footnote dialog.

If that isn't it, please let us know:
What version of Word are you in?
Specifically how are you inserting the Endnote?
Do you still get the endnote, just with the reference wrong in text and
note, or does no note space appear at all?
Do you have section breaks, and is this happening within a particular
section?  
Are you using a non-standard font where this is happening?

DM