How to prevent calendar alerts from becoming Drafts (???) in Mail.app?
Calendar invitations are delivered via email, so perhaps Mail app is preparing things for you to "accept, tentative, or decline" the invitations as part of the routine processing of a mail message that gets diverted from the inbox and places in another application (Calendar in this case, or iCal for those on Lion and earlier).

You could also just configure Calendar to not retrieve CalDAV events from Mail in the first place and let mail handle things in the inbox rather than having the system try to process things for you.


  Calendar -> Preferences -> Advanced 


Deselect the box next to Automatically retrieve CalDAV invitations from Mail