Was this an imported user perhaps? If so, I'd guess that the points total was incorrect at the time of import.
Any change here is going to require a manual database query. Assuming you only want to update specific users, you'd need to identify the user ID (in the URL of their profile page). Then you'd run this query:
UPDATE xf_user SET warning_points = 0 WHERE user_id = 12345;
Change 12345 to the correct user ID.
(We always recommend taking a backup before running any queries directly against the database.)