I guess you're talking about the classic versions, because I've seen it happen a couple of times on the current version.
First instance I can recall was on the $50,000 Pyramid. In one of the tournament episodes there were two men playing each other for one round. I have the episode in question.
In the '80s $25,000 version, in early '85 they had a blind contestant week and there were two men in one of the games.
In Davidson's version there was one tournament episode where it happened.
It almost happened on Clark's $100,000 version. Two men qualified for one of the tournaments but they never got to play each other because their female opponent kept winning.
Other than that, I don't think there were any other occasions. Kind of hard when 80% of your contestants are women!