My sister is flying DCA-JFK-SFO. I upgraded her to J from JFK-SFO.
When checking in her bag at DCA, the machine said $0 (expected) but the printer jammed. She went to the counter where she encountered "an extremely unpleasant guy" who insisted that she had to pay $40 for her bag. Looking at her baggage tracking, there are 2 tags, one that says scan unavailable and one that is en route. I suspect that she got charged $40 as it's the second bag vs. $30, even though she only has one bag?
Regardless, given she is in J on JFK-SFO, her bag should have been free. To ask for a refund, do you go to prefunds.aa.com or Customer Relations?