I just ran into the same issue. But first, make sure that you didn't actually unlock him. In this game, you unlock magneto but you still only see a black silhouette. He's on the right about halfway down. You go to his spot to see how much he costs, then you have to buy him.
But if you've already tried that, then you may have hit a bug. I'm on the xbox one. I uninstalled the game and reinstalled it, and it kept my progress AND made magneto available. Which was great because I was crushed when I couldn't use magneto.