Avis deposit withheld

Avis at Cape Town International. I hired a car that already had 50 000km on. I got a flat tyre and changed the tyre immediately. I did not hit a pot hole or drove with the flat tyre so there can be no damage to the tyre itself. I took out a waiver for damage and Avis kept back almost my whole deposit claiming they have to replace the whole tyre. There was said to me that I got the car in perfect condition and returned a damaged car. Also that they don't plug a tyre, they replace it. I just don't understand why I must pay for an entirely new tyre if the car already had 50 000km on.