Final Fantasy 9 skill system

When the last monster dies, the battle ends - nothing can be triggered from that point. Truthfully, I don't see a way to detect if that last monster dies or is left behind in an escape.

And, again, if they run away, it'll just add the potential AP gathered so far because it simply has no idea whether or not you ran.

The best way to say this is to look at one-monster fight. You can't tell if that monster is killed or not - if you run, the battle ends without triggering anything, and if you kill it, the battle also ends without being able to trigger any "Monster is at 0 HP" events. You can either start with the AP (meaning that if you run, you still get AP), or you don't give AP at all for that monster.

This will happen with every fight, unfortunately - you just kill all but one monster, and you will have the maximum AP earnable from that fight. Then you can just escape.

Of course, the obvious way to get around this is to disable escaping for the entire game, but that's just annoying to the player.