When minecarts and boats are placed, when you leave the render distance several conditions can occur when you return. If the cart is on a track (any type of track, powered or not), if there is a mob inside it, the mob will be floating just above the minecart when you return. If the cart is not on a track, the minecart will be floating approximately half a block above whatever surface it was on when you return, regardless if it contains a mob or not. For boats, they will be floating above the block surface as well, regardless of mob status, but only if not in water.

Walking into/through the minecart or boat will cause the mob and/or minecart/boat to reset position.

This is not just a visual bug either, as one of my worlds uses the minecarts on carpets version of a villager spawner. When the minecart is seated properly on the surface, the child villager spawns in the area below the carpet. When the minecarts are floating, the child will spawn on top of the carpet. Replacing the minecarts with boats achieved the same results.

This has been tested in both survival and creative modes, on both a PC and XBOX ONE.

Further testing shows that if a mob interacts with the minecart or boat it will reset position as well (i.e. a second mob enters a boat with a mob in it, a mob enters an empty boat/minecart, or a mob bumps into a full boat/minecart).

Also, if a track (any sort) is placed below a floating minecart, it will immediately reset to the track as well, including resetting the mob position. I believe mincecarts already on tracks are probably still being floated up during the render distance transition, but reset automatically though the mobs are not being reset in this case for some reason.

Finally, floating mobs do not take suffocation damage if their heads end up inside a solid block from this condition, so their offset positioning my be visual in nature only.