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.
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Duplicate of MC-221, please use the search function to see if your bug has already been submitted. Currently over 51% of tickets are being closed as duplicate.