This is a Calendar issue, but it is also tied in with Mail. I have several users with MacBook Pro's and iMacs. Nobody on Mavericks is having this issue but the two users I upgraded to Yosemite are having this issue. (we are using Exchange V2010)
What we noticed is that when accepting or rejecting invitations, the Yosemite user replies get stuck in Drafts. We have to open the draft and manually send the email to settle the issue. Could be that your version is sending the drafts but not quite confirming 'sent' and does it over and over?
For the record, I spent almost two hours with Apple Care demonstrating this problem and its relationship to a message that says it is "unable to save the message" and offers to try again, revert to server or ignore. No answer resolves the issue. The user boards on these issues have more answers than Apple Care is able to provide.
This is the best repair I've found to date:
Open System Preferences>Internet Accounts, select the Exchange account and turn off Calendar. Then, go to Calendar>Preferences and delete the exchange account. Next. In the Finder, hold down the option key, click Go and Scroll down to Library. There, navigate to the Calendars Folder. Delete Calendar Cache and all the folders labeled with long strings of numbers and letters. Click on the Pending Events Folder and, again, delete all the folders labeled with long strings of numbers and letters.
Then, go back to System Preferences>Internet Accounts, select the Exchange account and click to turn the Calendar back on. Restart your computer.
That seems to clear out the problem. Until iCal creates it again...