Anti-Climax Boss: The final boss is rather easy to beat, but if you want to go for a Perfect Run (shoot every bullet thrown by the boss), that's a different story. Higher difficulty levels, however, will live up to the game's reputation.
Demonic Spiders: The centuar-like Seemers near the end of Stage 3-3 can deal heavy damage with their boomerang-like projectile that can sweep across the bottom or top halves of the screen and sometimes they attack at the worst possible time for you to dodge.
Narm: Saki's voice(s). He sounds like a teenager in cutscenes and dialogue, yet when you're in control of him and making him attack, take damage, and get knocked down, he sounds like a middle-aged man.
A lot of the voice acting in general is So Bad, It's Good, especially Achi constantly overlapping her own dialogue.
That One Boss: Transformed Achi - Earth Mimicry. Considering the bonus for this boss requires practically frame-perfect movement and aiming to stop any collateral damage AND that there's three ways to lose the fight (you die, time runs out, or Earth is destroyed by Achi...
It's sort-of balanced out by the fact that you'd have to be trying to lose before earning at least one continue, meaning you'll have as many chances to defeat the boss as you want.
Polestar at the end of 2-2, although that's more of a Noob Bridge than anything for those who have yet to figure out that auto-aim reduces shot damage.
That One Level; Stage 2-2, you constantly bombarded by gunfire by turrets from gunship cruisers that are both bothersome and annoying, you can easily miss the time bonus from the mid-boss roughly half-way through and time items don't show until further in the level, plus if you're trying to get a high score run, missing chance to slash the mothership's core will strip you of your entire stage clear bonuses.
Stage 3-2 can also be one since the controls were not made for a 2D side-scroller and you'll be fight the controls more than Ruffians.
Viewer Gender Confusion: Saki isn't exactly the most masculine looking video game character, leading to someone on NSider2's first thought on seeing his Assist Trophy update in the Super Smash Bros. blog, "Who's the chick?" The Wii U version of Smash 4 outright lampshades this.