How do you catch a fairy in a bottle
Everytime I try to press the y button I set the empty bottle to, it makes the beep sound, can I even use the empty bottle at all?
You need to use the Bug Catching Net to be able to bottle up fairies (as well as bees). Once you have an empty bottle, go see the Bee Man in Kakariko Village (inside the hut with the big bee sign), and he will give you the Bug Catching Net.