I've always thought of Rune and Passion augments as long lasting but once per session or scenario, but skill augments as being very brief (maybe just one roll) but can be thrown around like confetti. Maybe. If it becomes a problem, maybe only use it to augment skills that are below 50, or that are likely to be knocked down below 50 by opposed skill contests or other modifiers. And if the players complain that that is unfair, well, just tell them "I never roll augments for NPCs, I haven't got the time, so watch out or I might just..."