I finally completed my playthrough of this fantastic game after taking my sweet time (180+ hours). These are the more serious bugs that I bothered to write down and that haven't already been mentioned elsewhere - fixing them would make for an even smoother experience:
- It's possible to permanently lose the airship (game-breaking) by doing the following:
-- Landing directly east of Lindblum Castle (two tiles), then entering the castle.
-- Landing on Surgate (the eastern tile), then entering the town.
-- Landing on Citadel (the two central tiles in the top row), then entering the town.
-- Landing on the Tower of Trials (upper tile only), then entering the tower.
-- Landing on Lenadia City (every tile except for the entrance tile can be landed on), then entering the city.
-- Landing on Meksicburg (left or right building tile), then entering the town.
-- Landing on Cornelia (left or right building tile), then entering the town.
-- Landing on the clouds above Everlasting Tangle (i.e. the forest in which it's located), then entering the location.
- It seems the turn counter for certain status conditions (like Stop) isn't reduced (by 1) each turn.
- Despite having a Pearl Rod (+100% KO resist) and a Ribbon equipped, Elina once fell victim to a Death spell (Beyonder hunt).
- After Vahn has jumped or used "Dragon Dive" (and is already in the air), he can still be hurt by attacks from confused units (confirmed only for ally units). Units suffering from "Berserk" can hurt a jumping Vahn, too (confirmed only for enemy units).
- Lyric's physical attack skills "Gambit" and "Jackpot" can only target herself.
- Gozmodan's Grotto: One of the treasures (sparkles) spawns inside solid rock outside of the player's reach.
- Ivalice Checkpoint, eastern entrance (when the entrance is blocked): When talking to the left guard from above, the game freezes (the actor is pushed back one tile, where the path is blocked by a jar).
- Lenadia City, entrance map, southwestern area: The player can easily get trapped by NPC Abby (by cutting into her walking path).
- Zen, western area: The player can easily get trapped by NPC Daisuke (red clothes) by standing on the far right side of Daisuke's walking path.
- When the player is supposed to revisit Branch Castle after having obtained the airship: Entering Branch Castle through the dungeon cave lets the player revisit the old version of Branch Castle (instead of the new version that is needed to advance the story).
- I think the sparkle west of Duncan's Dojo (during the game's first part) can't be reached, since the player never has access to a Chocobo in this area.
- If the player reenters Citadel Sewers from Citadel Dungeon during the game's second part, the sewers will be restored to the version of the game's first part.
- A nameless (empty/unusable) item (a staff listed between Merlin's Staff and Poison Staff) can be stolen from Cyallarus enemies in Trabia Base (second version).
- Dragon Point: Players can easily get trapped (up and below) by the walking NPC in the western area (between the beds).
- Spare Change enemies (30000 HP) can't be defeated, they're immortal (once they reach 0 HP). Might or might not be intentional.
- Cave to the Underworld: The Underworld entrance/exit of the cave is bugged (i.e. the cave can't be entered from the Underworld). Thankfully, the player can ask the Moogle inside the Inferno Chambers (after defeating the boss) to transport them to the surface.
- Not really a bug, but the remaining unwinnable boss fights (apart from the already fixed one against the "Entities") could still use a little tweaking. Our favorite dragon, for example, can be stun-locked (when the player has obtained "Bad Breath" for Ami as soon as possible) while whittling away at its 1000000 HP, and it can be defeated even faster by using Vahn's "Stock Break" skill (which reduces its HP to 1, since it's not immune to this skill's effect). Furthermore, it's also possible to survive (not win) the unwinnable boss fights at the Water Shrine (second visit) and in the Elemental Abyss - and to get permanently stuck by siphoning all of the enemy's MP.
Thanks again for a really great game, it was a lot of fun to reach the ending and to discover so many secrets along the way.