According to The Collider's Comic-Con Looper panel recap:
Gordon-Levitt was asked what it was like to work with Emily Blunt, and he sited her ability to make him laugh as a big plus. He added, “most pretty girls aren’t funny.”
Yes, he was trying to compliment Blunt but at the detriment to the rest of her sex. Between Adam Carolla, the sharp debate on if Girls was comedy, and Vanity Fair's editorial on why women can't be funny because biology, this has been a rough time for funny ladies.
Twitter was not amused when Levitt's quote started to leak out: