If it was a Go-Light fare, you'd be entitled to a bag each as a result of your *G status, and the third bag would indeed be chargeable.
If you were definitely not on a Go-Light fare (and this has nothing to do with fare basis - Go-Light can be applied from the less to most flexible fares), then you were incorrectly charged and should be asking A3 for a refund.
Were your FF numbers in the booking and reflected on your Boarding Pass? And was it a separate booking for the domestic flight?