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I've only had one time when the AI got in the way of a capture - I gave Mite to Swaine who used Cut Loose at the start of the battle, and because I'd already downed all of the enemies using Earsplitter that killed the one which was waiting to be Serenaded. I decided to remove Cut Loose from him then and it hasn't happened again.
I've had this happen a lot while stealing, but not too often when capturing, though it has happened.
The AI when set to "All defense" (which you really should do if you're trying to get golden glims at least) will not always JUST defend. They will also, for some ungodly reason, cast defensive buffs and healing spells as well.