Tim, what are the assignment's settings? Is "Require students click submit button" ticked?
You can do a report to see what Moodle thinks happened. Left side nav bar under "current course"> Reports > Logs > change "All activities" to the name of your particular assignment > change today's date to "All days"> make sure "All actions" is selected > Get these logs
The result will show you students in "User full name" column, submissions in the action column as "assign submit," and in the Information column as "Submission status: Submitted for grading. the number of file(s) : 2 file(s)."
That tells you Moodle thinks there was a submission. But, be aware that standard Moodle reports don't show deletions. It is possible to be a student and go back into the assignment and delete the file, not that I'm accusing your students of gaming the system. I've only had one occasion of this in the last 5 years.
