Yes! The rust is from the outside of the BB, onto your BB shell. The Ultegra BB is sealed, so there's no maintenance necessary. I found the same thing on my brother's bike when I was cleaning it for him. When I took off his BB, I notice some rust an water on in the BB shell from a downpour we were in 2 weeks prior. I drained it and wiped off the rust in the BB shell and BB, itself. There was no problem with his Ultegra BB though, just some rust that was easily wiped off.

Now, your clicking sound may mean that you have a bad BB or the LBS may have put in a non-sealed BB on you bike. This can get water in the BB. Regardless, if it's the BB that's the problem, it's the BB manufacture's problem (Shimano), not Trek. Your LBS need to contact Shimano about it. Heck, your LBS should just replace the BB for you and then work on getting the BB warranty. The BB is $40 and you've spent $2k+ on the bike. That's the least your LBS can do so that you don't have have to deal with this crap.

Don't unscrew the cable guide on the bottom, that's not there for that purpose. You may mess up your shifting, if you do that since both the front and read der's sit on it. You can do what others have suggested and take off you seatpost and turn your bike upside-down or buy the tools to properly remove the cranks and BB to drain and clean out the BB shell.