He sucks bad at that. He's an awesome coach, personnel evaluator, QB developer, X's and O's schemes guy, outcoaches almost everybody he plays. But he is not super at challenges. It seems like he just throws the red flag if he doesn't like the call. But you have to throw it if it has a chance to be overturned. If it has no chance you just lose timeouts which can cost you in close games.
Don't get me wrong Harbaugh is the best thing to hit the Bay Area and 49ers in a long time. And I love having him. I would not want anybody else. But maybe he could get better at that. He reminds me of Norv Turner here in SD. Who just throws the challenge everytime he doesn't like the play. No matter how many times he loses or loses timeouts.