This problem appears to be caused by corrupted Calendar caches and it occurs in macOS 10.12.2 Sierra as well.
The easiest way to get rid of this problem is to:
- Quit Calendar
- Open Activity Viewer and Quit "CalendarAgent"
note, using QuickLook on any calendar item in the Finder will relaunch CalendarAgent which needs to be not running at step 3
- Delete ~/Library/Calendars/Calendar Cache
- Delete ~/Library/Calendars/Calendar Cache-shm
- Delete ~/Library/Calendars/Calendar Cache-wal
Calendar will read the information from the surrounding data folders and files in ~/Library/Calendars/ and recreate the caches cleanly.
If for some reason the files listed to delete re-appear before you launch Calendar, it means something is triggering the system calendar operations. Try quitting all of your applications and starting at step 2 or logging out with the "Reopen windows when logging back in" unchecked, then logging back in.