Originally Posted by The Goron Moron

Also there's another thing missable in LA. The game requires that you need Bow-Wow to eat those flowers in the swamp area if you want to get into the Bottle Grotto dungeon. However after beating that dungeon and returning Bow-Wow to Madame MeowMeow, Bow-Wow can no longer be used and the flowers cannot be destroyed. This makes getting optional chests in that dungeon missable.

There's also a chest containing some rupees in the swamp area as well, blocked by another flower.