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Looks like the total list of affected skills are:
Drill Kick (missing Crono's Cyclone damage contribution)
Volt Bite (missing Crono's Lightning damage contribution)
Bubble Snap (missing Marle's Water damage contribution)
Spin Kick (missing Robo's Robo Tackle damage contribution)
Bubble Hit (missing Marle's Water damage contribution)
All of these are due to that character's damage being forcibly excluded from the attack in the original game...
Falcon Hit isn't bugged, but it does look like I wanted to give it a higher attack power at one point, and didn't know how to at the time. I gave it 200% Spincut damage, which is what it had in vanilla, but it looks like I originally wanted to give it 1.25*Rock Throw and 1.5*Spincut. It could probably stand to be better than 2x Spincut, but 1.25*Rock Throw and 1.5*Spincut does sound pretty... formidable... for an AoE attack, even if it is limited scope AoE. And those are pretty strong attacks being used for its base, at least for that point in the game. I'll have to think about how much power I'd want to give Falcon Hit.
I checked triple techs, too, but none were affected.