I believe the phrase is used to mean something like "the fact that you found something that is obviously an exception proves that the rule normally applies."

For example, imagine if your skydiving instructor said "if your parachute doesn't open when you jump out of the airplane, you're gonna die", and you replied with "well actually that's not true, Vesna Vulović survived a fall from high altitude." Yeah, okay. The fact that you had to be smarty-pants about it and dig up a random exception really proves the point they were trying to make.