I'll check the logic and see if there's a way to get it confused there, but it might have just been bad luck. Also, there are two keys - if you've already opened the chest in the glade, a second chest appears in another area.
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Opening the boxes unlocks some otherwise-hidden content elsewhere! As the game expands, I want to keep including reasons to go back and explore places you might've already been to see what changes; the chests are an early example of that. In this case, the zones to check after opening them are the Hot Springs and the Grove.