Well, the AI chooses the target with the most HP overall or the most dangerous one currently. So if a goblin stack has the most HP, the AI will attack it. A way to remedy that is to cast awaken dragon and summon another Lightning Orb, which will surely hit it.
It's a bit dodgy, and you should be aware that you can't get 2 orbs to attack the same enemy, but they can take out quite a bunch of units in one go anyway.
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