Generally there's supposed to be a cool-down timer that prevents the enemies from immediately using the hypno command once he recovers, but it could be glitching for some reason. The trouble will be finding a way to reliably reproduce it so I can zero in on it and know when it's fixed. How often is it happening for you, and can you get it to happen frequently and reliably? Also, double check you're on 0.3.2, just to be sure we aren't looking at an old bug.
Let me know if you're able to zero in on it. I did a basic sanity test, ran through the scenario a few times on a fresh save, but no luck. Unfortunately if it's not something that's happening frequently, or easy to reproduce, I'll probably have to leave it for now. RPGMaker's scripting and interface is kind of all over the place, so at a certain point I have to settle for "good enough." But let me know if you're able to get a closer lock on it.