Water In rear end

Hi
I have a 2012 Frontier Pro 4X The truck has never been off road or in water.
The abs light came on soon I took it to the dealer. They replace the rear axle breather tube but said there was water in the rear end, and it need to be replaced. They asked if I had a boat and I told them NO. The said that the truck must have been in water, I told them never I bought it new. I had heard that if the breather tube was block this could cause condensation causing water to be trapped in the rear end, but the refuse to cover it under warranty and want $5000;00 to fix it the truck has 41000 Kms

Has any one had or heard of this happening

Thanks