Also, a lot of Enemy Skills can only be found on monsters in the Crater (Pandora’s Box being the main one, which is only cast once by only the first Dragon Zombie you encounter), so it’s worth going through the Crater several times to get everything.
So if you missed anything on your way through there the first time, then you’re out of luck sadly, as the crater is completely different when you go through there as the final dungeon in disc 3.
I presume the Enemy Skills you’re after are Trine, Magic Breath and Bad Breath right? Trine is tricky (one of the trickiest skills to learn), but can easily be gained in disc 3 if you haven’t done the Pagoda quest in Wutai (simply equip all Enemy Skill materias you have that lack the spell to Yuffie when she faces Godo at the top of the Pagoda).
Magic Breath however is used by the Parasites in the Crater in disc 3 so you can easily gain it if you missed it the first time. Likewise with Bad Breath – Malboros are quite plentiful in the final dungeon so their signature spell can be gained later too. 😉