"should" is perhaps the right question, however in California the answer is "does it?".

I don't know if you live in California, but "permits" are the go to weapon of neighborhood activist groups to try to get what they want. Whether it is to prevent building, property use, or nuisances. My guess is that someone argued the container is a "building" (it has windows and a door after all), and every city requires that you get a permit before you put a building on your property. Whether it is a lowly garden shed or a guest house.

Should neighbors be able to attack each other with the municipal code? That is a pretty deep question. Do they? Sure all the time.

This particular container is attracting vandalism where it sits, arguably a quality-of-life issue extending beyond the property line. Dunno about the general case. This particular case here gives no reason to argue that permits in general are a case of government overreach.

Should is up for debate, but many places require a permit for an RV or shed, so a shipping container probably does.

Just to be clear, you are arguing that all land, regardless of topology, existing use and zoning, and adjacent interest is equivalent, right?

Honestly? Maybe. Depends on how long it's there and what it's used for. It can negatively effect both my quality of life and my financial situation. You don't have a right to do that.