Anticlimax Boss: The Vampire is significantly easier than the Time Warrior that you fight immediately prior.
Demonic Spiders: The Scissor Crabs in Enrich Dungeon... much tougher than other enemies (and is in fact a multi-stage enemy with multiple targets), can very easily kill off your healer and are surprisingly common. Worse is that they initially appear at a time when you don't have spells that can hit multiple targets at once.
Aura/Praying Level 4: For a modest MP cost, it fully heals your entire party. Once you acquire this spell, you practically can't be killed conventionally.
The Kusanagi: A katana sometimes dropped by a monster in the final dungeon (Spike Dragon), this weapon allows Rodi and Akane to occasionally one-hit kill most monsters (except bosses and Evil Bodies) with a Critical Strike, including the two minions that support Rilix in her second appearance. Getting even one makes most subsequent encounters a complete pushover... getting two just gets ridiculous.
Goddamned Bats: In every area there was at least one enemy that could seemingly summon an endless supply of reinforcements. Each Battle could have up to six enemies on the screen at once so unless you manage to kill all six before one of them does so you're in for a very long fight.
It's not all bad though - you get a hell of a lot of experience when the fight finally does conclude, especially the Strikerpods in Enrich Dungeon.
That One Boss: The King Snail. Even if you've overlevelled this boss is insanely tough.