Nobody but a fool does that kind of business deal without verifications. There are companies you can pay to inspect, verify and insure the product at source.
To me this screams like an inside job. How is it possible that the thieves can get into the ships at night, spend hours hauling copper and paving stones and nobody notices.
The article also mentions shipment. Does it mean the containers were already on the ships, or just on its way on the back of a truck? It would be "easy" for the truck full of copper in a sealed container to leave a place, and a different truck to show up at the port with a container with a label that says "Copper for Mercuria, destination Qinqdao" and a "good" seal. Or if it's all at the port, just pay off the crane operator to load up your bogey onto the ship, and load up the real stuff onto your truck.
From the article
It appears that copper was initially loaded into the first shipment of containers, before being surveyed by an inspection company. Seals used to prevent fraud were then affixed to the containers.
The product was real and loaded into shipping containers. After it was inspected and sealed the fraudsters switched out the cargo as it left the port. There was even Insurance fraud with some group providing fake Insurance coverage (one real policy with the rest being forgeries) for the seller.
These firms aren't fools, they do this everyday and understand what to do, shit happens.