Filling up to the first click is always allowed. No one at Hertz ever goes beyond the first click when refueling themselves.
It's probably a really simple mistake but so many of you want to have your conspiracy theories. Hertz, at least when I worked there, used a very dated program. The OP said he drove 95 miles. Well, with rentals under 100 miles, that can cause a problem. There are two questions that have to be filled out at return by the agent...if the customer refueled and whether or not the tank was on full. Well, if you put that the tank was on full but forget to change that the customer refueled because it is automatically a no...it charges a per mile rate. It does this because in theory, if it is a low mileage rental, then it can still be full even if the customer said he didn't refuel...so if the answer is still left at the default 'no' then it charges a per mile rate.
More than likely, it's an error on the return agent. Also more than likely, not intentional.