In the rune battle minigame, you're presented with two sets of runes (yours are on the right, the enemy's on the left), each of which has two symbols in it. You have to choose the rune from your set which has no symbols in common with any of the runes from the enemy set. There is no time limit, so simply find the single rune in your set whose two symbols are unique relative to the enemy. For each battle, you'll have to repeat this a few times, but it is very easy as long as you are patient and observant.