I have had this experience multiple time two years ago when COVID changes were causing havoc with scheduling booked flights. I learned that the magic words after making the booking changes which had to go to ticketing were: 'I need you to confirm that the price we agreed on is the actual ticketed price' or some variation thereof. The agent seemed to understand what I meant. I had noticed that on a previous rebooking involving a payment, the ticketed price was not the same as the price I was quoted on the phone.