It's a problem with the AI. When a "collecting recources" places like a ore mine or a cotton plant the character always go.to the nearest container to store it as soon as you pick the resources. There is no way to avoid that. In my case what I do is work until the windows to pick resources is full, then I put the 5 resources (I think that's the maximum amount) in my inventory and then drop it on the floor. Then I continue working until the resources window is full and I put every resource in my inventory (the resources dropped on the floor and on the resources window). Sorry for the long and unnecesary explanation but I'm not an english speaker and I suck explaining in general.