Disappointing Last Level: The final area you fight through in Relentless. Not so much the final confrontation with Funfrock, but the path leading up to it after destroying the cloning facility is pretty dull. It's just a long boring mining road which includes one particular rage inducing point where you have to get by an invulnerable Dirt Excavator enemy with absolutely no room to work with.
Game Breaker: Magic spells in the second game breaks it in half with no shame. It might be the reason why the Big Bad is so damn set in getting it!
The Ring of Lightning in the second game when used as a weapon is so overpowered it can One-Hit Killthe final boss of the game.
The Protection Spell is just as overpowered if you choose to grab it from it's Bonus Dungeon. If you're quick enough at killing your enemies, you could possibly complete the game without ever taking any damage if you always keep your mana up.
Aggressive stance with the sword. Never miss a swing, and you basically have your enemy stun-locked.
Gameplay Derailment: In the Desert Island theme park, there's a small raised land area that Twinsen can use to jump off from to get into the hole for the money reward without having to complete the duck shooting game.
Goddamned Bats: And Goddamned Fireflies in Zeelichian undergrounds.
Good Bad Bugs: The famous "jump-save bug" in the second game.
For the first game, the fact you were able to hurt yourself by running into things in the Sporty stance was a pain for a lot of players.
For both games, knock-back is an huge annoyance since it's possible to get stuck in a never ending knock-back loop until your eventual death.
Aggressive stance's attacks leave a bit to be desired. Twinsen can either throw a quick punch or wind up a slow kick which leaves him wide open to retaliation and, as stated above, some enemies can put Twinsen in a long loop of damage and pain.
That One Boss: The flying seal on Mosquibee island. You have to use a leather baseball glove to throw back the fireballs the seal spits at you. And you have to use a precise angle to make it work.
That One Level: The Mosquibee lair island, with lava galore. Thankfully, it is only optional.