FLL and MIA, as far as I know, are not co-terminals. So, if an agent queries for availability YUL-MIA, s/he won't automatically get the availability for FLL. So I guess you can't really blame the agent for not checking FLL because s/he might not have known that they are close together.
And as for waiving the change fee..... I guess you'll have to do the phone-rounds, where you phone again and again until you get the answer you want.