In Summit, Using an armor kit does not remove a "Broken" stack while Fragile Armor Directive is active. My active Directives are; Cool Skills, Fog Of War, Fragile Armor, Hard To Earn, No Regen, Ragers, Scavenged Skills. On Heroic difficulty.
Thanks for getting in contact and providing this feedback, if possible could you provide an image or short video clip showing how this occurs in game and we will be sure to get this looked into as soon as possible.