But doesn't that seem to leave a problem where the airline can call it a mistake just not a big enough mistake that they would cancel them all them. Is AA going to send out notices saying you booked a mistake fare and you won't be getting miles or just not award them and make the member fight it out after the flights?

It would be bad form for AA to deny miles but never notify the passenger they wouldn't receive them and just refer to some obscure clause in their T&Cs.