A hertz rep at LAS explained to me that a recent system change means that the refuel charge is now automatically added if you drive < 100 miles. They now have to manually intervene to remove it, every time.
Perhaps the best way to deal with this without hassle if you return after hours is to just not fill up the car if you drove less than 100 miles. You might be out a few bucks but at least you won't be paying for fuel twice.