Well this was my thinking to the OP's post. Correct me if I am wrong on the matter. If your already allied and their is an alliance leader. Only the alliance leader can add new allies. Unless these guilds were allied to a faction BEFORE they were allied into another alliance, shouldn't the alliance leader have caught certain guilds friendly to them even factions?
I never had to deal with a situation like this so just trying to figure out how such a situation could occur in a mutiple guild alliance. I could see and understand if it was the blue guild and a faction only (like it used to be before the change of faction and blue guilds allying fixed by the devs),but in a big alliance I cant see it since the dev's supposedly fixed it. Plus if its being exploited again if it is an issue then somebody should of reported this to the dev's. Maybe I read and over thinking to much into his post but that was my take on it.