The 50/50 actor participated in a panel at the convention for his upcoming science fiction thriller Looper, also starring Bruce Willis and Emily Blunt.
Josh Dickey of Variety tweeted from the event, where Gordon-Levitt attempted to compliment Blunt by saying: "Pretty girls aren't usually funny."
According to Dickey, Blunt, who plays Gordon-Levitt's love interest in the film, visibly "bristled" at the comment.
Along with Looper, the 31-year-old actor will also star in The Dark Knight Rises later this summer.
A third film, Premium Rush, is due for release on August 24 in the US and September 14 in the UK.
Watch a trailer for Premium Rush below: