Oof, similar story-- years ago I visited San Francisco and pre-paid the toll of crossing the Golden Gate bridge twice in my rental car. For whatever reason the system only connected the pre-payment to my crossing one of the two times. For the other crossing, they tolled the car, which then caused Avis to bill me, which also triggered their daily 'convenience fee' of ~$4 daily, not just for that day, but for the length of the rental.
I tried to call the tolling authority but they blamed Avis, and Avis blamed them and so forth.
Their mistake ultimately cost me like $35 so after a while it just wasn't worth it to wait on hold and then argue with a brand new person every time but it still angers me when I think about it.
The moral of the story: Put a fake license plate on your car if you're crossing an open tolling juncture.