Ahh, I know what's the issue with Disarm now. The problem is it doesn't refresh properly - when I end with 1 Disarm on a level, then I get 2 on the next one, instead of the full 3. Which I assume is the intended behavior - so if you don't use them, they're essentially wasted for you for the next game. Or at least it seems to behave that way for me.
I also second the multiple flag types that were mentioned above; one for each type of mine would be great but might be an unnecessary overkill to cycle through them.