First, you can require them to send you the documentation. I did that when the charged me for a dent repair. However, unless you proof disputing their documentation, you're going to have to eat the charge if you can't negotiate it away. You've already knocked off all but $1 as it is.
Any rental company can charge you later for fees they incur as a result of your rental. I agree that ten weeks can seem long, but given processing times (toll authority getting info to Dollar, Dollar tracking it to your rental, Dollar charging you, you getting your statement), it's not out of the realm of legitimacy.
If Dollar is waving the $25 service charge (most companies will charge and administrative fee to collect), I would just pay the $ unless you can prove you weren't on the toll road that day or that you paid the toll. Without actual proof, it just becomes your word against theirs, and they claim to have the documentation backing up their position.
The likelihood of Dollar intentionally defrauding you is pretty slim, but my own experience of them is that they will definitely run charges through for anything out of the ordinary. If they wanted to pile on fraudulent charges, they would be pretty stupid to do it with state records (toll agency), which would get them in trouble with the state for using their information for fraudulent purposes.
Dollar's not a fly-by-night agency . . .
Dirk