I think it's because he's angry, which is somewhat understandable, because he thinks he's debating with a racist.
I'm not sure why he refuses to accept the fact that he might be wrong in this instance, though. I've seen him talk about other topics with Maher before and he's not nearly so bombastic or hard-headed.
I saw an interesting interview with Harris shortly after this where he said everyone was shocked that Affleck inserted himself into the conversation this way as well. I haven't seen many episodes of this show but apparently this segment is always a one-on-one between Maher and the guest in question, usually talking about whatever book or movie they're promoting, and given Ben's relative frequency on the show prior to this, he was aware of that.