If you don't think it's counter intuitive to use the skill that is unlocked by consuming a battle state only when you are back in that state I don't really know what to tell you.
I mean that's not quite how it works. Again you open the states, and then just maintain them. This only gets screwed up because the players involved don't understand the state system at all and aren't tracking it. If you don't have visibility on this stuff you're not going to know how to handle it. That problem is something that can be solved fairly easily by just giving a UI element similar to RK attunement or warden gambits that tracks combat states. The top tier players are already running such UI elements, whether it be from Auras, Prime, or Gibberish.
It's pretty easy to understand, people are just stuck doing it blindfolded because they aren't really aware of any other option. Just give them a proper class resource display and solve it.