By any chance are those possibly differentiated assignments where they have only been assigned to a particular section, group, or set of individuals in the class? I ran into this earlier in the year when troubleshooting a similar issue with a faculty member.
Without knowing much more about the behavior you're seeing, I'll suggest that Todd's recommendation is accurate. Do you use differentiated assignments in your course? If you do not assign an assignment to a student, that assignment will not be gradable for that student and the cell will be grayed out.
Let us know if you have additional questions!
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