Alec is a traitor
Several times he has quietly sabotaged the search for the Mortal Cup, particularly breaking the circle while summoning the memory demon and allowing Clary and Simon to be kidnapped by the werewolves. He's either secretly working for The Circle or is under secret orders to make sure nobody gets the Mortal Cup so long as Valentine is still alive.- Jossed. There is a traitor, but it's not Alec.
Alec's injury from the forsaken is the reason for his odd behavior
Think about it, he was completely normal the previous episode, but then as soon as he got the injury, he changed. He's siding with the Clave, acting up against his father, and going against Jace. And I think it has to do with the injury from the forsaken. Magnus has issues with being touched
It could be he's just not used to being touched, or maybe he's offended? If you look at any of the times in the first season, and season 2, he always looks down at whatever part of him's being touched. I just can't tell if he's surprised someone would touch him (outside of sex/flirting), or offended someone would do so.- Given that his mom killed herself, and what kind of childhood he would have had, it'a not unbelievable that he's still surprised when touched.
- The look of surprise isn't just reserved for touches. Magnus often says that certain parts of him are ugly (his character, his warlock mark, his past) and always seems surprised when Alec is gentle and accepting in response, as if he had expected Alec to lash out. Add to that the fact that Magnus' last big relationship was probably with Camille, and a pretty grim picture starts to form: This troper would like to suggest that Magnus' issues are due to his fairly recent abusive relationship with Camille, and not because of his mother's suicide. Traces of that relationship can still be seen in their interactions; Camille tells Magnus repeatedly that she is the only one who accepts him and cares for him, and he parrots those sentiments back when he tells Simon that she was the only one who cared enough to keep him from committing suicide. Convincing the victim that they are not loved, except by their abuser, making them feel as if they owe their abuser something because of that love, and making the victim see themselves as undeserving of love are pretty classic tactics in abusive relationships. Camille probably took Magnus' insecurities and dialed them up to eleven over the years, along with isolating him. And he still hasn't gotten these thoughts out of his system completely, Camille visibly gets to him every time she speaks. So this healthy, loving relationship wih Alec is a surprise for Magnus at every turn, because he had probably almost forgotten that this is what love should be like.
