The bug

A boat with two non-player passengers will have only one passenger when the world is saved and re-loaded, if the x/z coordinates of either passenger are in a different chunk than the x/z coordinates of the boat. (The saved passenger is the one whose x/z coordinates are in the same chunk as the boat.)

How to reproduce

In a single-player world, summon a boat along a chunk boundary with two passengers, then save the world and re-load. For example:

/summon boat 8.0 63.0 0.0 {Passengers:[{id:wolf},{id:chicken}]}

→ Upon re-loading the world, only the wolf will remain

Example

Here is an example in video: Boat passenger is not saved if it is in a different chunk than the boat.mp4