This occurs when a student isn't unenrolled from the classes after leaving. Rather, the student record was archived hiding them from the interface - this doesn't removing the enrolment as the Admin sync runs before the timetable sync, so when the timetable sync runs there's no student for it to unenroll.
Prevention: The only way to prevent this is to unenrol any no-shows or early leavers and run a sync. Then after that, archive the student record in the admin system and run another sync (or let the overnight sync run).
Resolution: Please report any instances of this to the SEQTA Service desk including the date-range for which the enrolment needs to be removed. It's not possible to remove past enrolments through the interface.