Not sure if this was ever mentioned before because I'm never really on here much, but I noticed that companions (the chocobo) do not attack any target if the caster uses certain AoE abilities. So far these abilities are ones that don't have a specific target like
  • Flaming Arrow (BRD)
  • Holy (WHM)
  • Blizzard II (BLM)
  • Circle of Scorn (PLD)
  • Flash (PLD)
  • Steel Cyclone (WAR)
  • Ring of Thorns (DRG)
  • Shadow Flare (SMN/SCH)
  • Miasma II (SMN)

tested all of these while companion was on free-stance, not sure if it's a bug or not just wanted to shine some light on it.