You could have asked to speak with the manager at the station, or go get them and show them the car.

In the end, the odds of you taking a car with a small scratch and putting a larger one exactly where it was on the damage report are a bazillion to one. Because you had a damage report showing damage, you will probably not have any problems explaining to them it was there when you took the car.

If you did not have the damage report it would be a different situtation.

I would call the return location and ask to speak with the manager about it. It's pretty stupid they were arguing over the size of the scratch.