Something similar happened to me in BOS in September. I canceled my Friday evening reservation on Friday morning, so you can imagine my shock seeing a statement of charges email as I'm waiting to board EWR-BOS 200 miles away from the car that I had allegedly just returned.
Since customer care was closed for the weekend already and that was supposedly the only department who could help (huh?), I went to Hertz as soon as I arrived in BOS to sort out the charges. No one had any power to wipe away the fraudulent record, but the shift lead zeroed the balance on the rental so I wasn't charged.
A call to customer care the following Monday also didn't get the record cleared, and just as I feared, I was charged for tolls several weeks later. A few weeks going back and forth with @Hertz on Twitter finally got the toll charges refunded.
The closest that I got to an explanation in BOS was that they had "System issues" that kept associating the same car with multiple reservations that day. At some point, customer care even confirmed that their car records show that I was not the driver of the car in question, a point that I can't possibly believe given the toll charges. The simplest explanation, which is a few mistakes in a row (car associated with canceled reservation, ID not checked when exiting lot), makes much more sense.