Uhhhhh.... Twelve is not flirting with Clara. At all. :/ He's being protective of her, sure, but the Doctor has always been protective of his companions. ...Cuz they're his companions.
As for not picking up on Pink, Twelve is just a little bit oblivious when it comes to such matters. That's all. Which is one of the reasons why I like watching him, actually. He even assumed that the guy dressed like Eleven was her boyfriend just because he looked like Eleven. Which was kind of amusing.
But yeah... there's no flirting going on between Twelve and Clara. Not sure where you got that idea.
Edit: Hell, he spent most of The Caretaker being a nuisance to her, and messing with Pink because he didn't approve of him being a soldier. That's not flirting.
Edit2: And he isn't getting in the way of her dates, either. Just... taking her on adventures like he normally would. He's even bothering to bring her back in time for her dates. Which is more than most Doctors would've done!