Yes, there was rust on the BB cartridge itself.

I'm not sure how it is a Shimano problem. I would guess Shimano doesn't make their BB cartridges to sit in a puddle of water that has nowhere to go. Or perhaps Trek should put out a warning with their bikes indicating that you should ride in any kind of moisture at your own risk and riding in the rain will void the warranty.

If I am making a federal case out of it, it is because having BB problems on a bike that retails for close to $3,000 within a month of buying it is not what I would expect. I know that when, in the past, I've owned Performance branded private-label bikes, Performance has stood behind them 100%. I have seen the guys at that shop replace things on people's bikes that were definitely user-caused. Trek is a manufacturer with a much more well-known brand. I can replace my BB for under $50 with a top notch Dura-Ace model...but that doesn't diminish the fact the I will have had to do so at my own cost on a bike that is 3 months old and was ridden in the rain a total of 4 times.