Check the flight numbers--- if the flight numbers stay the same on the return flight even though you have a stop or even a plane change, then Apple did nothing wrong. That is the way the airlines describe the trip. For example, USAirways Flight 46 starts in San Francisco, headed for DC. It stops in Phoenix on the way; technically they call it a refueling stop or something like that, but they pick up new passengers and lots of people stay in Phoenix and don't continue on to DC. Since it maintains the same flight number all the way, it is called a "direct" flight. That is just how the airlines do things. I don't like it either--- I'm a business traveller and I take that Flight 46 all the time and I get less airline miles than I would if the flight changed numbers but I have all the hassles of a connecting flight, it is the worst of both worlds. But it is what it is... anyway if the flight number is the same all the way through, you're out of luck. I suppose you could complain but I doubt you will get very far, and even if you do complain to Apple, they're just passing along the info that the airline gave them. Now, if the flight number changes mid-route, you have some arguing room and a room upgrade is a reasonable thing to ask for.
Just keep in mind that the FAA allows some loose descriptions of what is non-stop, and if the airline is showing it as a nonstop flight, Apple will not know any different.