An empty grade does not (always) equal zero!
The default setting for Moodle Gradebook is to not reflect empty grades in category or course totals. This allows students to see a running total of their current progress at any point in the course. Without this feature, if empty cells were treated as zero points - which would include all yet-to-be completed assignments, students would see an artificially low course total when they view their grades, until all grades have been posted.
To view this setting, click on Grades on the Moodle course page and then the Setup tab. Click on the Edit link to the right of the name of your category and select Edit settings.
On the Edit category page, under the Grade category section, click on Show more... if necessary to expand the section, and locate the checkbox for Exclude empty grades.
With Exclude empty grades turned on, wherever you want a student to receive zero points you must enter zero points in the relevant cells.
At the end of the semester if you don't want to fill in a zero for every missing grade, it is possible to turn this gradebook setting back on to treat empty grades as zero points. However, it is important to note that this is a category setting and needs to be set for each category and for the course. Changing this setting will also cause it to be set if you later import this course for a new semester, causing undesirable effects. Therefore, it is advised and often easier to manually enter the few blank grades in the Grader report view, or to bulk fill empty grades, as below.
Here’s a short screencast showing you how to access and change the setting.
Bulk filling empty grades with zero
If you want to use the Exclude empty grades default feature so that students will see a running account of their course grade total, there’s an easy way to fill in all of the blanks cells in a grade item with a zero (or any value you choose, for that matter). For detailed information, see Bulk editing a Grade Item in the Modifying Grades and Overrides in Moodle article, or view this screencast showing you how.
Hidden items
Hidden items in the gradebook can also yield misleading results. If your course includes hidden grade items, make sure to turn on the Show totals excluding hidden items setting. If you don't do this, and there are any categories that have hidden items, the category will not show a grade for that portion of the course. See Showing Totals in Moodle Gradebook for detailed instructions.
Student views - See what the students see
Moodle allows you to check the student view of grades in a course, or to see what a specific student sees when viewing their grades. For detailed information, see User Report - What students see in the Moodle gradebook. You have a lot of control over what is and is not displayed, and how point scores, percentages and letter grads are formatted.