Putting goods on a ship via the expedition menu seems to "remove" / block access to goods for the population.The supply at the residents goes down to 0% without any goods ever leaving the storage.
After unassigning the ship form the expedition, the supply goes up to 100% again.
The above video shows an example of this, where loading fish via the expedition menu does not remove it form the storage, but the supply at the houses goes down.
In this case there were only 50 tonnes assigned to the ship, with 72 being available, but the supply still drops to 0% without a single ton leaving the storage.
Workaround: Loading goods manually form the harbor and not via the expedition menu, does not trigger this bug.