Ass Pull: Gandrake's motivation behind his villainy. Actually, that entire scene is one big Ass Pull.
Not that much: apparently he's been controlled by a destructive goddess called Amestris (sealed in the Archnembulus) and manipulated. The fact that most of the information regarding her is almost cut out, though, adds to the confusion.
Contested Sequel: Brave Fencer Musashi was a pretty tough act to follow, but most gamers weren't expecting it to have a proper sequel in the first place (especially since Threads of Fate, released after Brave Fencer, is considered a Spiritual Successor of the first Musashi among its fans). Samurai Legend is said to be a decent and fun game overall, only paling in comparison to the first game thanks a bunch of little things that made the sequel worse: questionable voice acting, especially for Musashi himself, the camera and combat needing a bit of polish, and the story itself doesn't carry the charm of the original game.
Demonic Spiders: The red Ninjaroids, especially on the final level. But you'd better get used to them, as they're the focus of one of the few decent Level Grinding spots in the game.
Also some late-level foes like the Vapor Knights.
Narm: Not that big an offender, really, but it does have some overdramatic quotes. Especially in the scenes surrounding Mycella's death.
Every character that Mushashi has to carry usually has some contrived reason explaining why they're unable to walk. If you haven't figured out by the second carry that it's going to be a running theme, it can come across as really silly (or charming), especially since the game barely lampshades it (though at least one character pretends to be hurt just to be carried) and some characters actually start walking on their feet not long after Musashi gets them where they need to be.
Nightmare Fuel: The modifications Malbec gave Arachnolia are terrifying, to say the least. Not helping matters is that Arachnolia, as the name implies, is a Giant Spider.
That One Boss: Moltan, Arachnoblia, Asura and Nebulite Gandrake. Each of these is tougher in the arena sidequest, which imposes strict time limits. For some, it's best just to go level for a while and come back later.