My answer is based on the comment thread below your question.
In this comment thread, we have established the following:
- It is likely that the containers were decommissioned due to the police claiming it as evidence for the murders.
- Due to the nature of the crimes, the containers will have been considered evidence for a long time, so replacements will have been used by the industry (if replacements were needed at all).
- Given that the shipping industry cares little for what happens to an individual container (containers are interchangeable and relatively expendable, and they are only really useful when being shipped around), it's likely that these containers are not actively tracked by the administration anymore. No one was waiting for these specific containers to come back. If replacements were found, everyone stopped caring about the old containers.
- (not explicitly discussed, but implicitly accepted as a logical consequence) The police did not retain ownership of the container, and gave it back to the company that owned it after the trial.
- It's unlikely that the containers are in a "graveyard" for unusued containers, as Dexter has had to dodge workers to get to his container. This doesn't make it impossible, however. It's still possible for workers to visit the graveyard at one time or another.
On to my actual answer:
If the containers were indeed decommissioned, then it stands to reason that they are not administratively tracked anymore. This is a known phenomenon in warehouse systems. Anything that is not tracked can be ignored by workers for decades, as they are never looking for something that is no longer administratively known about.
Think about it from a business perspective. Who is going to complain about these containers?
They don't work in that zone, so they won't come across an errant container. And even if they did, why would they assume that the container shouldn't be there? Would they go to the effort of looking it up? It's not their job after all.
Employees are not tasked with checking all the containers that are in the container yard. Instead, they get given an order to fetch a specific container.
If Dexter's container is no longer tracked by the system, then the system will never assign a worker to look for this container.
Furthermore, a worker does not occupy himself by questioning every container that he comes across.
Why would he? It would take a lot of time and effort, for something that would hardly ever be useful to do, and no one expecting him to do so.
As long as the container is not in anyone's way, no one will actually be incentivized to ever move the container or question its presence.