If they are going to charge an administrative fee, I think I would tell them I demand proof of their claim, like photos showing car and license plate at a toll booth, not just somebody's printout and if they refused to send proof then I would dispute it with the credit card. Make them at least work for their adminsitrative fee ripoff.
The worst toll scam I have seen however is coming in or out of the airport in Dublin. There is a toll on that short stretch of road but no toll booths. There are signs that are easy to miss telling you about the toll but nowhere on the road itself to pay it. You have to get to the internet within as I recall about 48 hours and go to their website and pay by credit card. If you miss the first time period, the toll keeps climbing, a lot, through several other periods. If you search it out, there is a place you can pay at the airport itself, but again that is not easy to find. I imagine that a lot of people probably get nabbed on these tolls for not paying by the deadlines, and then rental car companies add on other fees, too. We were lucky in that at the welcome meeting at Knocktopher Abbey (DAE exchange), they told us about this and the office helped by going on the internet and entering our rental car license plate and cc info within the first deadline. They also told us where we could pay in the airport (not easy to find) for the return trip.