The Course Navigation indicator represents the number of changes in a course since your last visit. Currently, this feature is only used for Grades.
Sometimes a user wants to know what has changed since the last time he or she has visited a course, especially with Grades. The numbered indicator for Grades shows a user either a change in a score, including new scores, or a comment left on a submission by an instructor or a peer.
To clear the indicators, view the Grades page. When you refresh or navigate away from the page, the count will reset.