While none of the big things in the game are missable (Stray Beads, Brush Techniques, upgrades and Gold Dust), there are a few minor things that are missable. There is one dog when you go through the Spirit Gate in Yoshpet that you can miss feeding, so your Animal Tome won't be at 100%.
The following dungeons are one-time only: Moon Cave, Imperial Palace (when you are tiny), Oni Island, and the area beyond the Spirit Gate. Note that there is one enemy that you can miss while traversing the Imperial Palace dungeon (Fire Doom Mirror), so make sure you purposely go after the scrolls later on in the dungeon to get this enemy in the Bestiary. There are 3 clovers in Moon Cave, 3 in Imperial Palace, 1 in Oni Island and 11 past the Spirit Gate (3 in Kamiki and 8 in Shinshu). The Dragon Palace dungeon may be missable, so you should get the 4 clovers there, too. Other than that, only common items are missable.
There is one small sidequest that is missable in North Ryoshima, which involves Yoichi the Archer. You'll notice him firing at a fruit hanging from a tree. Use the waterspout technique to connect the water to his arrow and it will make the fruit soft. You'll only miss 30 praise, so it's not that big of a deal.
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