Whose responsibility is it?

I received a car from the dealership about two weeks ago. At first the finance/bank wanted to void and null the contract because the paperwork wasn't sent to them. Today, the bank called and said that contract was a go because they had received the paperwork from the dealership. They also wanted to know basic things about the car, but I couldn't tell them cause the car has been in the shop for the past week and a half (transmission needs to be fixed). Also, today the warranty company called and said that I was responsible for the cost of the transmission being fixed because it was sent to an unauthorized specialty shop. I told them I wasn't paying because I sent it back to the dealership and the dealership sent it to that specialty place to be fixed. I want to know who is responsible for fixing and paying for the transmission. Keep in mind that this car has a 90 day warranty and this falls well within the 90 days.

Thanks for any responses :)