FF2 is a big game with a bunch of stuff - most of it you can get at any time. There are some things, however, like bestiary mobs and treasure chests that go away forever. With keeping spoilers as minimal as possible, I'll be detailing when to stop and make sure you get everything.

Ok, here we go in order of encounter:

Below, I'll outline all the keywords so that you don't miss any but first, dungeons and monsters:
Missable Enemies List and Missable Items
Phorusracos - Outside the dreanought before you board it
Buccaneer - when you get to control a boat on water
Kill fish - same
Sea snake - same
Hell diver - same
Land ray - East of the desert/in the desert at any time before the tower
Antliion - in and around the desert at any time before the tower

Warning ** Completing the Mysidian Tower dungeon changes the World map spawns. Before doing that, be sure to have the above enemies killed. Ok? Ok. **

Additionally, make sure you have the chest from Altair before then too. Its hard to miss.**

Once you have access to the wyvern go to Paul's house at the SW of Fynn and ask him about the Cyclone. go into the secret room near his bed to pick up 8 chests you otherwise would miss forever.

Palamedica Castle is not only a one time dungeon, but also home to several enemies that are gone forever once it's gone. While there, hit these guys up:
Skull
Eyemoeba
Black knight
stone Golem
General

Missable Dungeons list
Dreadnought - get all the chests before leaving or it's GG.
Leviathan - 5 chests inside, get them all before beating the boss.
Cyclone - Get all the chests before leaving.
Palamecia Castle: get all 17 chests.

Jade passage/Pandaemonium end the game - but you can leave at any time by casting teleport. Do this to wrap up any non-missable items, such as monsters and chests still chilling in the game.
Completing the game puts you outside the final dungeon but saves your progress - so you don't have to be afraid of clearing the game.


Keywords:
Start of the game, Hilda grants Wild Rose

Returning from Fynn/Scott: Hilda grants mythril, dreadnought and airship. Cid can also grant airship in paloom or w/e city he's in.

After the bafsk Cave incident, Go to poft and ask cid about sunfire.

Next, talk to hilda about sunfire and then the king - and ask him about the godesses bell.

After dreadnought, talk to gordon on the throne to learn about Dragoons and wyverns.

Before Retaking Castle Fynn, Make sure you visit the forward Camp
It appears when you rescue Hilda in the Colosseum and disappears when you take back Fynn.

After retaking the castle of Fynnigan, Ask hilda about Mysidia, Masks, and ekmet teloess.

Ask Gordon in castle fynn about ultima

Make sure to talk to paul about Ekmet Teloess to get to the sewers dungeon and get all the castle fynn chests at this time.

After the cyclone ending Scene, meet with hilda and learn Palamecia.

After Palamecia Castle, ask hilda about Jade passage.

(as an added bonus, fly to castle deis and ask the woman about dragoons to get exaclibur - not a keyword but awesome sauce)

Altair HildaWild Rose
Altair chest
Altair Hilda 2 Mythril
Altair Hilda 2 dreadnought
Altair Hilda 2 airship
*I had trouble finding the goblin prince on the 1f of the keep you get sunfire from, in the post game, so potentially make sure you grab him here. IDK if its a bug or I've got terrible luck.**
After Bafsk Cid sunfire
Dying King Godesses Bell
Phorusracos & Dreadnought Dungeon Chests
King Gordon altair Dragoons
King Gordon altair Wyverns
Buccaneer
Kill fish
Sea snake
Hell diver
Antlion Land Ray
Pre-Retaking Castle Fynn, Visit the forward camp as suggested - Its a missable map location.
Castle Fynn HIlda - Mysida, Masks, Ekmet Teloess
Castle Finn Gordon - Ultima
Unock sewers via paul in fynn city for chests
Leviathan Chests
Castle Fynn Hilda - Learn Cyclone
Talk to paul about Cyclone, get the wyvern
Talk to paul about cyclone again, 8 secret chests in pauls room
Cyclone chests
Talk to hilda to learn palamecia after cycleon
Palamecia castle chests: 17
palamecia enemies:
Skull
Eyemoeba
Black knight
stone Golem
General
Ask Hilda about Jade Passage
Talk to dragoon lady about dragoons at castle deiss
Wrap up everything else before completing Pandaemonium if you wish (teleport gets you out if need be and beating the game just makes it a pain to go back through Pandaemonium for 1 or 2 missed mobs.