Sounds like the delete process didn't wipe the entry properly from the database - has this happened before?
I'm guessing you'll have to delete the faulty submission from the moodle core database manually. If you have DB server experience great, if not then contact your support personnel. Here's what someone will need to do, step by step:
1) SELECT id FROM mdl_user WHERE username='usernamehere'
This will get the numerical id for the username you specify (i.e. the student who's mark is to be deleted).
Keep this result in your head (or on a postit note) as useri
2) SELECT id FROM mdl_assignment WHERE name='Assignment's EXACT name here'
This will get the numerical id for the asssignment - you MUST type this exactly how it is named in moodle.
Keep this result as above as assignmenti
3) SELECT id,grade,submissioncomment FROM mdl_assignment_submissions WHERE assignment=assignmenti AND userid=useri
This will give you the id number of the row containing the students entry (and show their grade and comment the teacher made when marking it).
Keep the value of the 'id' field as submissioni
MAKE SURE THIS IS THE CORRECT ROW FIRST!
Assuming it is...
4) DELETE FROM mdl_assignment_submissions WHERE id=submissioni
Hope that helps
Clearing assignment feedback and grades
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