they don't fit, because 'yes' was not supposed to be used in the context of 'yes it is a mistake', yea was. Having two words helped stop that ambiguity.

It's confusing because it was stated wrongly.

https://en.wikipedia.org/wiki/Yes_and_no#The_Early_English_f...

Yes contradicts the negative question. So "Is this not a mistake?" should be contradicted with "yes, it is a mistake" or affirmed with "no, it is not a mistake".

It's further confusing because we have the idiom of suggesting things politely in a tentative manner such as isn't this a mistake? which has lost its sense of negativity and has come to mean "this is a mistake, I think," as opposed to being parsed literally to mean "this is not-a-mistake, I think".