Here's one that's more of an event oversight.
If Terra is dead before entering the Returner hideout and meeting Banon for the first time, she stays dead even after resting before she's supposed to go around and talk to everyone. Before you tell Banon you want to be the Last hope for the Returners, you can venture back out to the field with only Terra and she still has zero HP, so if you enter battle it is game over.
And another bug with non-standard battle endings:
If Terra is Morphed when Gau returns from battle, her sprite will change back to normal (without ending Morph). In this case, the supply will not be updated, unless her Morph timer runs out before Gau starts talking; she will then perform Revert and the Morph supply will be updated correctly.
Non-standard battle endings are their own can of worms because they seem to skip over several routines which are supposed to run when a battle ends. With Banon dying, it's not much of an issue since it triggers a game over anyway, but Gau Leaping or returning can cause item loss. When an item is selected for use, it is removed from inventory immediately. If that turn is canceled because the battle ends, the item is supposed to be returned to inventory. In the case of Leaping/returning Gau, that doesn't happen. I assume it's the same if Banon dies, and possibly with other battles ending via event, such as Kefka in the imperial camp or on the bridge, or sketching Ultros 3.