If an instructor uses the gradebook plus 'Edit Grades' tab, and there is an assignment with student submissions in the same category that's being edited, all of the assignment submissions will be updated and given a zero grade.

To reproduce -

Create an assignment and have some students upload submissions.
Go to the Edit Grades tab, and assign a grade to one of the students.
On the assignment submissions page, all of the student submissions will now show a grade of 0 instead of 'no grade', the 'Last Modified (Teacher)' column shows the current date/time, and the 'Status' column shows 'Update' instead of 'Grade'.
Students also get an email saying their assignment has been graded.

Even worse, if the instructor is editing a grade for something other than an assignment (a gradebook event, quiz, different assignment, etc), any assignments that happen to be in the same gradebook category will inadvertently get updated.