I would look at the date the assignment was turned in versus the date it was due, and the settings for missing work. Canvas has an option to assign a 0 (or some other grade) to any assignments that are missing, after the due date has passed. Let's assume that you (or your district) has that option turned on. It is in the Gradebook settings, by the way.
Assignment A is due on Monday at 11:59 PM. On Tuesday, Canvas assigns a 0 to anyone who has not turned it in.
A student turns in the assignment on Tuesday afternoon. Hypothetically, Canvas should remove the 0 and mark it as late. However, there is a flaw in the Canvas system. Once a 0 has been assigned due to the missing work setting, that 0 will remain EVEN after the student has submitted late work. This is really annoying when you have it set up to Sync with your SIS nightly. Issues with the Missing flag have been reported for several years at least now.
Three ways to fix this. Go in and manually remove 0's from anyone who has turned it in is one way, the second is to remove the setting to automatically apply a grade for missing work. The latter will prevent this from happening, but it you would still need to manually fix any 0's applied before turning off the setting. Grading the work will also remove it, obviously, as the third fix.