I actually deal with this problem far too often. What usually happens is that Hertz switches a PlatePass into a different car but does not update the computer, so PP thinks your car (original license plate #) is accruing these tolls.
This has only been an issue for me at local HLEs (NYC), but it is extremely annoying. You will need to contact PlatePass by email and explain the situation. I am lucky to be using my own EZ Pass, which corroborates the mistake PP is making.
Sometimes, at first they agree to reverse the fee but not the tolls (as if the PlatePass inadvertently captured tolls instead of my EZ Pass), but with an angry follow up email, I am able to get a full refund.