These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: Leader's Force aren't just called that because each member thinks s/he is the leader. It's also because their purpose is to lead Musashi to the Five Scrolls.
Fridge Logic: Concerning the ending, which has a text only introduction that announces something along the lines of "To Stop This Ever Happening Again, The Legend of Brave Fencer Musashi will be told eternally", and then in the following end scene, We have the Princess covering up the whole thing from her Parents, the King and Queen. Think about that for a second. If that is intentional, then no doubt, this is Fridge Brilliance.
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 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.