Before planting a Magic Bean in a mound of soft dirt, empty a jar of bugs (you can buy them for 50 rupees at Hyrule Market or just find them under rocks) on top of the mound. Catch one of the bugs mmediately afterwards so you don't have to find or buy more of them. After one of the bugs goes into the mound of dirt, a Gold Skulltula will jump out, except for the mound right next to the bean selling guy.