Every container comes with free time — a few days to collect it, and a few more to give the empty back. Miss either window and a charge starts running, per container, per day, until the box moves. On a delayed shipment these are usually the largest unplanned cost, and they are almost always avoidable.
The confusion is that three different charges sound like the same thing. Two are billed by the shipping line and one by the terminal, and which one you are paying depends on exactly where the container is standing.