What is the purpose of the empty bottle?
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Buy the empty bottles whenever you come across them as they can be filled with either health or stamina potions when you find the woman selling the potions out of the two huge cauldrons.
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While the answer above is correct, it leaves out important details as well. The empty bottles can also be used to catch bee’s you find under bushes or amongst the enemies in a room. I’ve not seen one yet but I’m sure that if you see the fairies flying around you can use the bottle to catch them as well , just like in main Zelda titles.