I've had problems like that with Indranel and some others. Just end the mission and restart it and then WAIT for about 5-10 seconds before you press the weaken enemy button and it should work. I was pressing it too quickly (right after a cut scene or something) and it was weakening them to 1/1 HP but making them invincible. So just wait a few seconds and then press it and everything will be ok =)
It's also possible, albeit incredibly drawn-out, to use "mega unit" on the boss to make them killable. It takes a really really really really really long time to kill them, though. Like, really long.