This Seeking Tech tutorial will show you the general locations of every permanently missable enemy in Final Fantasy III Pixel Remaster.
Nepto Dragon (Bestiary Entry #198)
The Nepto Dragon is easily missable as there is a special trick to adding it to your bestiary. You can only encounter this enemy before you beat the Nepto Temple. Instead of heading inside this dungeon, you need to ride the ship upwards to the canal to trigger the fight. During the encounter, you need to run away. If you managed to escape with at least one party member alive, then the Nepto Dragon will be registered in the bestiary. If you like to, you will be able to re-fight it again at any time from the main menu.
Killer Fish (Bestiary Entry #31)
The Killer Fish is one of the many enemies you will encounter in the middle sea section of the Floating Continent. Make sure you defeat one before you fly your airship over Saronia, since you won’t be able to explore any of the seas afterwards.
Hermit (Bestiary Entry #32)
The Hermit is another enemy found in the middle sea section on the Floating Continent. You need to defeat one before Saronia.
Sea Elemental (Bestiary Entry #33)
Also exclusive to the middle sea of the Floating Continent is the Sea Elemental enemy. You need to find and defeat one before you lose the ability to set sail.
Tangie (Bestiary Entry #34)
You should also encounter the Tangie at some point in the middle sea area of the Floating Continent. Make sure you have one defeated before Saronia.
Sahagin (Bestiary Entry #35)
The last of the middle sea enemies found on the Floating Continent is Sahagin. You need to beat one of these before heading to Saronia.
Anet (Bestiary Entry #71)
On the many seas located on the outer edges of the Floating Continent, you will be able to fight Anet. This enemy will disappear once you lose the ability to sail.
Mermaid (Bestiary Entry #72)
The Mermaid is another enemy you will find in the outer seas of the Floating Continent. Make sure you add it to your bestiary before going to Saronia.
Seahorse (Bestiary Entry #73)
The Seahorse is the final common enemy you can encounter in the outer seas of the Floating Continent. You need to defeat at least one before Saronia.
Sea Serpent (Bestiary Entry #74)
The Sea Serpent is a rare encounter in the outer seas of the Floating Continent. You should have a better chance of finding it in the seas of the second world. You must get this bestiary entry before going to Saronia.
Pharaoh (Bestiary Entry #66)
Castle Hein is a one-time dungeon where you can only fight the Pharaoh. So make sure you beat one before finishing it.
Lemur (Bestiary Entry #67)
Another enemy that can only be found in Castle Hein is the Lemur. Make sure you add it to the bestiary before beating the dungeon.
Lamia (Bestiary Entry #68)
You can also find the Lamia in Castle Hein as well. You need to beat one before completing the dungeon.
Demon (Bestiary Entry #69)
The Demon is also exclusive to Castle Hein. The enemy will disappear along with the dungeon if you don’t add it to your bestiary in time.
Dullahan (Bestiary Entry #70)
The Dullahan is another enemy that can only be found in Castle Hein. You will most likely find it in the small room on the third floor with a chest that contains the Royal Sword.
Ogre (Bestiary Entry #156)
The Ogre is an exclusive enemy in Doga’s Grotto. You need to defeat one before beating the bosses and leaving this dungeon for good.
Cyclops (Bestiary Entry #157)
You will also find the Cyclops in Doga’s Grotto. Make sure you add it to your bestiary before leaving the area.
Nemesis (Bestiary Entry #158)
The Nemesis is also exclusively found in Doga’s Grotto. Beat it before leaving the dungeon.
Humbaba (Bestiary Entry #159)
The last enemy that can only be fought in Doga’s Grotto is Humbaba. You should add it to the bestiary before you get locked out of this location.