Penny uses an analogy from the Star Trek movie to try and cheer up Sheldon. Throughout the entire series, however, she makes no secret of the fact that she finds the Star Trek series boring. If the boys weren't at home to take her to the movie, why would she have gone to know that plot detail?
When the guys return home after being away for three months, Leonard unlocks the door, they enter, and all the lights are on. However, Penny has always had access to the apartment and may have left the lights on the last time she was in there.