“The experiment included sandwiches from three Subway shops in Los Angeles.”
The article goes on to note that other tests have confirmed tuna in the, er, tuna in different locations.
The most likely explanation is that the Subway franchisee operating those shops in LA got cheap and didn’t want to actually pay for tuna. Few Subways are corporate stores, almost all of them are independent franchisees and Subway doesn’t police them anywhere nearly as well as they could. Not the first time a franchisee (in general, not just Subway) has played fast and loose with ingredients to increase profit margins.