Later, Harbaugh stopped in the middle of a question about something else to reiterate: "I realize I'm on the side of the 49ers. I'm the coach of the 49ers. There is some bias there, but I wouldn't be bringing it up unless it was obvious. But that's not the way they saw it. That's the only reason I bring it up."
He didn't need to go back and re-iterate the fact that he didn't agree with their calls right in the middle of another question. But it's in his nature. He complains all the time - either on the sideline, in press conferences, wherever.