Right now, if you were to have a storage crate with all the slots filled up (a variety of items but not the max of each), the game lets you auto-fill more items from barrels into your crate, but only the ones that fit, leaving the resources that don't fit on the barrel without notifying you by any means that there are more resources inside, but they simply don't fit on your crate.
The game should give a prompt near the fill prompt saying that there are unpickable items inside, as for right now, there's no way of knowing that unless you open the barrel yourself, removing the entire reason of using the auto-fill feature on long journeys of getting supplies.