How to make calendar notifications work in Sierra
I'm seeing this problem too, though it's inconsistent and only impacts my iMac. My MacBook Pro always gets all my calendar alerts, and both are linked to the same Exchange and iCloud calendars. I have tried fully re-installing Sierra on the iMac, which helped for about a week. Sometimes the missed notifications will trigger later (15 minutes to an hour later), but sometimes they'll never trigger.

There is a temporary fix I found:


Open System Preferences -> Internet Accounts
Select any account that has a calendar
Uncheck that calendar, then immediately re-check it


All of your pending or missed alerts will trigger at once! They'll keep working for another day or so. I'm in the process of reporting the bug to Apple at bugreport.apple.com now.