I don't know if it's normal that the game work this way, but seems that the game sometimes put groupable items in the proper container, sometimes not.
More not.

When I loot food, it almost never goes in the field supply bag. Same for keys in the keychain, and all other groupable items.

Something strange happened also for money, In the Reithwin Tollhouse. Every gold loot you take, it occupies an empty slot in the inventory.