We've found a few inconsistencies in Calendar, but most of them specifically have to do with meetings. To save time I'm not going to hunt down all the URLs, but I'll summarize briefly before getting to the issue that may be responsible here.
We've filed bugzilla reports about ZCO (and only ZCO) causing some instances of recurring meetings to disappear when the organizer updates the meeting.
There's also a bugzilla report about instances of recurring meetings persisting on an attendee's calendar, if the attendee modifies the meeting (by adding an alarm, for example), and the organizer then changes the recurrence pattern.
The only issue I've found that specifically has to do with an event reappearing after being deleted by the user is:
Bug 46918 – Deleted instance reappears after mailbox reload or server restart which has been fixed in 6.0.7.