Breather Boss: Kojiro. He is very predictable in comparison to the Crest Guardians. No wonder why Musashi barely notices him.
Guide Dang It: The Special series of action figures - especially Jon's, which requires that you hold off on opening exactly ONE treasure chest until after the game is beaten. Try to obtain the correct Gondola Gizmo on the first try using only the clues given in-game - though there's only two that match the requirements, and a degree of Trial-and-Error Gameplay is permitted.
The above is wrong, you merely have to get every chest to get the Jon & Leno figure. People use to think this was true because too many people missed a chest in the restaurant basement or the one on top of the mountain (and it didn't help that a plethora of rumors rose out about getting that figure and D Lumina 3). Once one person found a method that worked repeatedly, just about everyone clung to his method, despite the fact the truth was even simpler (and despite the fact that those that did miss those chests, still never got the figure).
The calendar puzzle on the first playthrough. The solution is on an item you got near the middle of the game and the puzzle is in the Very Definitely Final Dungeon. Before this, there is absolutely no purpose to the item so most players probably forget about it by this point.
Scrappy Mechanic: The platforming can be very annoying in the beginning due to occasionally sub-optimal camera positioning and Musashi's short jump range. Obtaining the double jump does much to alleviate this problem.
Seinfeld Is Unfunny: Hard to believe that this amount of voice acting in a video game was considered impressive; it was seen as such at the time because 1998 was the year when voice-acted dialog in console games started gaining prominence.