All airlines operate dupe check algorithms that will ID double bookings. Usually the booking is not cancelled automatically, but the reservation gets a remark that the booking seems to be dupe and will be cancelled within x hours or by y if the TA doesn't contact the airline with an explanation. If thereservation was made directly with the airline, you get notified/asked by the airline.

A lot of TAs make 'fake' dupe bookings to hold space on flights, even ticketing the same. Airlines of course don't like this, as their revenue/load forecasting is distorted by this.