There are a few bugs with specific attack animations and I somewhat know how to fix them. Apologies if any of these were already reported, I'm too lazy to look through the whole thread.
Fly: When used in battle, Fly's first turn animation and message are skipped and it's as if the attacker doesn't do anything on the turn. The move functions perfectly fine otherwise.
I found that this is because of a faulty animation call code in PokeBattle_MoveEffects in the Essentials script under Fly's function code, near line 4900.
Code:
@battle.pbCommonAnimation("Fly",attacker,[COLOR="Red"]opponent,hitnum,alltargets,showanimation[/COLOR])
I changed it to
Code:
@battle.pbCommonAnimation("Fly",attacker,[COLOR="red"]nil[/COLOR])
After that change it's been working properly for me. I have no idea if this is a proper fix since I don't know anything about scripting, I just copied how other common animation calls were done.
Aerial Ace: I know this has been mentioned before, but whenever an opponent uses Aerial Ace, its sprite temporarily disappears, causing some weird occurrences with the battle system.
Example: I choose Weepinbell to use Stun Spore, but opponent is faster and uses Aerial Ace, which is enough to bring Weepinbell's HP to 0. Opponent's sprite disappears. Weepinbell's fainting animation is skipped and the party window for replacing the fainted Pokémon comes up. I send out Empoleon normally and the opponent reappears, but before the turn ends Empoleon uses the Stun Spore Weepinbell would've used it didn't faint.
Anyway, to the actual problem: the fault is with the attack animation OppMove:AERIALACE. While the opponent's sprite does persist throughout the animation, there is no cel labeled "1" in the final frames of the animation, which is probably why the opponent's sprite disappears after the attack animation.
I fixed it by copying the cel "1" from the earlier frames to all the frames so that it exists throughout the whole attack, although just having it in the last frame might be enough. I had to copy the cel because although they can be renumbered, you can't number the cel 0 or 1 even if 0 or 1 don't already exist for the frame.
Icicle Spear: This is more of a minor nitpick as it's only cosmetic, but might as well report it. Icicle Spear shows wrong animations from second hit onwards because there are no separate entries for Icicle Spear hits 2-5. This would be easily fixed by copying the Icicle Spear animation 4 times and reordering the animations so that the additional hit animations are right after the original animation, but I can't find an easy way to reorder them.