I can't believe none of you have noticed the one of the biggest continuity errors that this film leaves us with. And it has absolutely nothing to do with X3 or Origins, but Singer's own films. An inconsistency that leaves an entire gaping plot hole in X2 and completely unravels the entire movie!
In X2, Magneto says he helped Charles built cerebro. It is what the entire film hinges on, Striker torturing Magneto to get information about cerebro, where it is located, and how it works. With that information, Striker infiltrates the X-mansion, steals cerebro, and uses that as the plot of the film to destroy all the mutants. In fact, Magneto's vast knowledge of cerebro even allows Striker to create blueprints of it to make his own before he even steals the real one.
In this movie cerebro is only a prototype and Magneto had absolutely nothing to do with how it is made. He doesn't know the inner workings of it at all, let alone to allow a mastermind to craft elaborate blueprints of his own cerebro 35 years later. And even if someone wants to create a trumped up version of how Magneto would know how it works, that was only the prototype and it looks nothing like the cerebro in the X-Mansion, whose location Magneto would also know absolutely nothing about.
Only way to retcon that would be to make a sequel in which Magneto and Charles becomes friends again and they spend a long time together building a beta version of cerebro that they place in the x-mansion...like that's going to happen. Magneto did not create cerebro with Charles as he says in X2.