Help please!

I have a 2007 Scion tC. Recently the check engine light came on. I took it to the dealer to haave it check. They said my carbon filter (I think) was filled with gas and I needed a new one. The reason it's filled with gas is because I top my tank off and the vapor/exhaust tube from my gas tank is above this filter. So when I top it off it just drips down in it.

Now they say my warranty does not cover it because I did it. When I asked how was I supposed to know they said it's in the book. (No it isn't.)

Has anyone else had this problem? Or do I need to take it somewhere for a second opinion?

By the way, I paid $500.00 today and my car has to go back in on Friday to have the part put in.