I have tested this in the snapshot, but I believe that it has been happening in vanilla as well. If you put a villager in a minecart quit your minecraft and relog in, the minecart and villager will have separated. This bug has been affecting one of the minigames I am working on where I use the minecarts like a car with a person in them. Please fix this so I don't have to kill them when they get out. It is causing bugs in my minigame.
Thanks for a great game as well as using Jira which is an amazing bug tracker.