Factual error: At the very end of the show, Leonard and Raj arrive at the hotel, which is supposed to be in Geneva, Switzerland, to visit CERN. If you look out the "hotel" window, it looks like they're half way up Matterhorn, but in Geneva there are no big/rocky mountains anywhere near the city itself.
Continuity mistake: Penny asks Sheldon if the roommate agreement contains something about girlfriends, which Sheldon dismisses as unrealistic. However, it was revealed in season 2 that there is a cohabitation rider. This was revealed when Sheldon asserted that Leonard's girlfriend, Stephanie, was officially living with them.