If an entity is riding a minecart or skeleton upon chunk unload, it will not store this in an NBT tag and will separate when the chunk is reloaded. A possible fix for this could be to assign a NBT tag that defines the persistent entity ID of another entity to continue riding. This also includes the player riding a minecart, saving and quiting and returning to be out of the minecart.
Related issues
Comments
fuj1n
I can confirm that entities do not stay in minecarts when chunks reload. To combat this I made the minecarts move back and forth to recapture the entities. This worked however I encountered a new glitch where the entity could sometimes look like it was still outside the cart and would be frozen in place. If I broke the cart the entity would suddenly pop out from the carts position.
For the case when the chunks are unloaded and entities leave minecarts, ensure that the minecart is on a rail, for player, this is intentional. (Entities dismounting could also be intentional, but before, they used to stay in the minecarts so long as it is on a rail.)