I had something very similar to that happen to me a day ago, I was doing some testing for my hack and after Cecil used the Crystal Kain proceeded to use it as well. 
No clue how I triggered it, wish I had made a savestate because my attempts to reproduce it today failed.
Edit: Got it to happen again, seems to happen anytime anyone is casting magic when the crystal is used.

Almost makes me wonder if the Avenger was supposed to make Cecil auto-use the crystal in this battle...probably just a glitch caused by berserk being removed and reapplied constantly though.
Perhaps, but the latter explaination (which is the same one I came to) seems to be the issue. The auto-use thing is usually done for an entire battle (auto-battle)... so it's not possible.. and I don't think anyone checked the Avenger Sword for the buggy behavior (I've only tested one version, but I'm sure it lingers in other versions.. and there was a specific fix for it in FF4A as an obvious hint to its overpoweredness). The best you can do is like the Golbez-Rydia summoning situation and "summon" Rydia out of hiding...
I do think the auto-Berserk effect while retaining the previous weapon's attack power is arguably the best abusive thing you could do for this game (free Cecil Berserk ignoring Crystal Armor's Berserk resistance late game == insane damage dealing).