How should a student deal with personal criticisms from an assistant professor? I am a PhD student. In the past I have met with an assistant professor for some general advice about my research, both times he has made off the cuff comments on my lack of competence as a researcher and overall career suitability in academia. During my continuation, he made further comments in this area. I prepared for 3 weeks solid for my continuation (or transfer or confirmation, in my case, it's like the defense of the first paper) and it went terribly. I can take constructive criticism and I welcome it, so as to better my paper. However, his behaviour I feel is inappropriate, as the focus should be my paper, and not my personal qualities.   

I am not sure what to do, if I should even do anything at all. In general, I consider my PhD progress to be very good, and my supervisor as far as I know shares the same sentiment. 

I'm cautious to respond to the  assistant professor, because he tells me I am being defensive, but then I am cautious of being too silent because he tells me I am not contributing enough. 

I have not spoken to my supervisor since my continuation or told him about my past encounters with this professor. Do I express my disappointment and confusion in our next meeting, or do I just leave it? I am lost on what to do, and I feel very deflated now.
He may be competing with your supervisor. He may not like your general topic. He may not like you. Or, he really believes what he says. Or he wants to test you. You don't know.

You have to live with people who confuse what's going on with prejudice- or agenda-coloured "truth". Practically all successful researchers have encountered such put-downs. 

Schechtman (later Nobel winner) got a "Introduction to Crystallography" book put on his table when he first reported that he got a 5-fold symmetry, hence quasicrystals, in his experiment. Feynman got put-down big time initially by Oppenheimer and was only saved by Dyson's aggressive intervention.

You think your progress is good? Your supervisor does, too? That's enough for you to go on, then. This guy may be a big shot, but for you, it doesn't count. Big shots are usually right when they think something is cool/great. They can be awfully wrong when they think something is not good. Trust your instincts.