There was no, "Let's talk about foreign policy," or "Let's move to the topic of Syria and US involvement there."
Should he have handled it so it wasn't a problem? Of course. All he had to say was "What do you mean?" And a friendly interviewer would have said, "I'm trying to find out your policy on Syria." And Johnson could have said, "Oh, I thought you we were still talking about the electability of third party candidates. Here is my position on Syria..." A friendly interviewer might have made a joke about it to diffuse things, but the MSNBC guy said, "You're kidding." That's made a gaffe into a viral gaffe.
True cringe-worthy events like that require two things: A gaffe and a hostile media.
Gaffe: Not making gaffes is an acquired skill of lawyers, seasoned politicians, and PR people. You don't have to be a rocket scientist to have the skill, and you don't have to be a lawyer, etc., to be governor. I have worked with very smart people with post-graduate degrees who put stupid stuff in writing all the time (not at my current company, of course). Any lawyer will tell you this. Gaffes are not an indication of intelligence. And, not having gaffes is an indication of learned discipline...something Johnson didn't have.
Hostile interviewers: Johnson had a reputation for NOT being a policy wonk in general, and they knew he was a non-interventionist (and so therefore likely did not know all the details of ongoing interventions), and they knew he didn't have a policy staff like the two major parties provide for their candidates, and they knew he wasn't good at this.. So, asking an interventionist question in a cryptic way hurts Johnson. Even with Johnson's ridiculous, overly-trusting, self-exposing response, the interviewer didn't have to embarrass him (and wouldn't have embarrassed him if he liked him).
Having said all of that...Johnson is kind of a goof ball...and I say that as a former Libertarian Party member. Lots of socially challenged people in that party.