In ‘Love is a Devil’ when Alec let himself fall from the ledge of the building, Magnus made it there just in time to catch him. But what it’s interesting is that he arrived there way before the others did and they all left the bedroom together after the thing with Jace and Maryse. So that means that Magnus must have ran up the stairs as soon as he heard Clary calling Alec’s name. He must have know something serious was going on with him. And that’s why later, when he fights Iris and she asks for mercy, he spits a furious 'After all you’ve done?“ I think that was the main reason he was so angry (and of course what happen to the others and his spell book getting stolen).