Actually, Magneto in the movies has affected various types of metals, showing a high versatility in what he can manipulate, and there's also a moderate to high percentage that the TF's have some of that metal in them, or at least if not, the metal is able to be manipulated via magnetism.
Saying that they are ancient aliens with advanced tech, a bunch of experience, and immense knowledge, which automatically makes them immune to Magnetic manipulation is not a strong argument, it's putting together a vague statement in the attempts of making yourself seem right without having to explain anything.