Normally traits you get from the class you're building off of don't count against the maximum number of traits you can have. If one of the traits you build off has Mercenary Class, how are you affected by the -Discipline from the prior class?
It looks like in the Confederation, the -1 Discipline was passed along to the Merc Captain since Merc Infantry was 1 trait over the maximum (Traits: Martial+1, Merc, plus 2 armory = 4 > 3).