Villagers in minecarts that have fallen a great distance die in midair without landing on anything, as if they had taken fall damage. I haven't tested the bug with other mobs, but it probably applies to them as well. To reproduce, put a villager in a minecart and push the minecart off a rail significantly higher than is required for the villager to die of fall damage.
MC-98286
Mobs in falling minecarts die in mid-air
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Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.