When a mob is in a minecart and travels into unloaded chunks the mob is not rendered in the minecart but standing on the rails. You can not interact with them on the track and will float when the blocks are broken beneath them and the minecart will continue on the rail. If you try to hit the mob as if they were in the minecart they will not take any damage but they will take damage when shot at with an bow and arrow or suffocating in a block. When the minecart is broken the mob will teleport to the minecarts position.
Look at vid to see how to reproduce >> https://youtu.be/c8ycXhz-jIk
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Are error messages described in MC-90683 in your Game Output
?
Same problame in Minecraft 1.9.2
Confirm for 1.9.3 pre-2 and I get this warning message in the Game Output [Client thread/WARN]: Received passengers for unknown entity
At least related to MC-96954.