INCORRECT ODOMETER, OVERCHARGED& UNALLOCATED REFU

I initial booked a car for three day and fully paid for as I completed my online booking. On the day of the pick up I requested to change drop off date to a day earlier which gives me a credit for a day. When I pick up the car the assistant advised that he's going to only hold R2726 since I had a credit of R1274 to make the required R4000 holding deposit required. I dropped off the car which I travelled 803kms out of the 800 free kilometers. I realised my cheque account is been debited and when I call to find out they told me I travelled extra 88kms which I disagree with. Apparently the extra R1274 has mysteriously disappeared and that's the money(R4000 deposit) they should use to deduct the petrol, tolls and extra kilometers from. I need some intervention regarding this matter.