Sounds like the charge was for a prepaid rental / no show fee on that rental. And, when your son went to pick up and they were out, the counter agents did not cancel out the reservation nor override any No Show penalty that was charged.

If possible, I'd contact them with you both on the phone together and start threads with their customer service via their website forms and social media.

If they were truly out of vehicles for which you had a prepaid rental, they may have some responsibility to your son's higher cost of rental at Alamo too.