Upon reloading a world that had boats that were summoned with with multiple passengers, only the boats' primary passengers still existed. Any further passengers that were in the boats were seemingly deleted.
Ex:

 /summon boat 0 6 0 {Passengers:[{id:"pig"},{id:"creeper"},{id:"creeper"}]}

In certain cases with multiple secondary passengers, not all of the secondary passengers disappear.
Ex:

/summon boat 0 6 0 {Passengers:[{id:"creeper"},{id:"pig"},{id:"creeper"}]}

This only seems to affect summoned boats, other entities with multiple passengers reload fine.