If a student emails an assignment rather than submitting through the assignment tab in Canvas, the missing submission badge appears. Once the instructor manually enters a grade for this assignment in the gradebook, Canvas should eliminate this badge from student notification.
| Comments from Instructure|
This idea is relative to the Priority: Gradebook Enhancements.
There were also recent updates to how the current missing/late feature exists. For more information, please read through the Canvas Beta Release Notes (2017-09-25) .