Calendar notifcation not disappearing
The badge is notifying you of a Calendar notification. There are two cases which causes a badge:


You've been invited to an event.
An event on one of your shared calendars has been modified.


To clear the badge, open Calendar and click Notifications  on the toolbar, then take action on the notification by selecting Accept/Decline/Maybe on an invitation or OK for a change notification.

Also see What&#39;s this button on Calendar.app? regarding the Notifications button on the toolbar.