The one I hate the most is from "The Cage", when Pike, exasperated over his flustering yeoman, says "I can't get used to having a woman on the bridge..." then looks over at Number One, "You're different of course, Number One."
I understand the historical and cultural context, and GR might have even thought he was being progressive about pointing out the woman on the bridge...but in the 23rd century, that would be something new and remarkable? That just seems anachronistic even for 1964. And condescending. And it's not as though she was being incompetent, she was just...nervous, like any young officer on the bridge of a starship might be when it was clearly her first assignment. I don't know, it just always bugged me.