Unfortunately, I don't think you can do anything about it. If the fare is not available, it is not available. The itinerary is not a ticket, and until you are ticketed, you don't have a leg to stand on. It sounds like you were never ticketed because the fare wasn't available. In fact, it's possible the fare was never available to begin with...since you have discovered they continue to advertise it when it's unavailable, maybe they were doing that all along.
I agree that they should not advertise a fare that is unavailable. In the future you should probably stick to more reputable travel agents.