Only two bad strikes, according to Pitch F/X -- one each to JBJ and Pedroia. In fact, JBJ stood and watched four pitches go by in the strike zone, and should have been out without even seeing a fifth pitch. That being said, the strike three call was brutal.
Pedroia got jobbed, plain and simple.
However, I agree with those posters who talked about protecting the plate. In that situation, you can not strike out. Once you've got the two strikes on you, you've got to be thinking about fouling off the tough ones, dumping one the other way, just plain making something happen. Not hoping that the umpire will magically stop calling strikes on pitches off the plate.