(1) Colbert mentions it bothers him that Snowden claimed he leaked in order to let us know how then NSA was spying on us, but then a lot of the information revealed turned out to be about how we were spying on others. Leaking that sort of info would only be justified if one is specifically opposed to us spying on other countries - and Colbert thinks the case for that position hasn't really been made.
(2) Somebody asked what Colbert sees as the likely endgame for Snowden. Answer: Colbert guesses the guy will probably come home in the end, but it's likely to take ten years before public opinion shifts his way enough to allow that. As an example of an analogous situation, Colbert brings up the Americans who fled the draft and were eventually pardoned by Ford and Carter.
The only reference I heard made to Snowden was in the very last question where an audience member asks Colbert how to keep people from being afraid of the government. In his reply, Colbert asked if what Snowden did was illegal, and when the audience said yes, he essentially said one of the bravest (and most morally admirable) things Snowden could do after breaking an unjust law is to face trial and accept the resulting consequences. His position came across to me as a combination of civil disobedience and traditional stand-and-face-the-music thinking. He didn't at all come across as vitriolic of Snowden or deeply offended by Snowden's actions.
Here's the video:
http://www.youtube.com/watch?v=bP9qqdE4O1I&t=1610