I often have problems in Florida with my NY EZPass. In Orlando one or two tolls failed to read and was charged (by plate) to the rental agency, but showing proof of other charges that rental on my personal EZPass got them to waive the admin fee. More recently was in Miami - all the I-95 express lane tolls billed properly to my account but NONE of the Airport Expressway (SR-112) tolls did (2x in each direction). Per my research, all Florida tolls are supposed to be compatible with EZPass, although that wasn't the case a few years ago. I believe there was also a change in administrator on the Miami-Dade highways so I wonder if that's part of the problem. I still need to send in my info to National, and I expect them to credit the admin fee, but I'm still overpaying for tolls.
There's definitely shady business going on in Florida, but that's really no surprise.