Issue:

The Schedule template has been removed from user's profile but still the discrepancies show up on the timesheet.

Solution:

This issue is related to Permissions. In the edit permission page, click on the (+) sign beside Scheduling and uncheck the option 'View Schedule Discrepancies on Timesheet'.This will resolve the issue as this option usually causes the discrepencies to show up on a timesheet even if a "blank" default template has been assigned.