I don't believe it was the AoE that removed stoneskin. The turtle died just as the cast finished. The AoE animation would have stilled displayed (since animations act independently of actual effect, ask any PLD or WHM about HG or Bene for a lovely conversation about this phenomenon). Most likely your stoneskin was depleted due to a crit auto-attack that occurred right after the AoE was finished casting, but before the enemy died. Not all auto-attack animations show because of an animation heirarchy this game uses. It always prioritizes skill animations over auto-attacks to make things look smoother and more natural, but auto-attack damage can and will still be dealt (by you or the enemy).