Within two months of taking receipt of our new 2006 Rav Limited we too were making nesting ground for mice. After discovering mice droppings, I started to set traps. After bagging 7 mice in four days, I put poisoned feed inside of the car. The mice ferried off three bads of poisoned feed to their nest in the cabin air filter (not recommended as we were then fumigated in the cab whenever it was driven).
We took the car back to the dealership and told them that they had to fix the problem or buy back the car. They were apparently aware of three locations where the mice can get in the car - two in the rear of the car and one up front in the cabin air intake. They put in some windscreen material in all three locations and we haven't had a mouse problem since. (they also cleaned out the cabin filter from the poisoned feed).
Unfortunately, I do not know exactly where they put the screens and I haven't taken anything apart to inspect. Because the dealership knew exactly where to put them, your dealer might also have access to this information.
Good luck with your dealership. There is no excuse for a mouse problem in a new car.
TLG