Fruit flies will naturally be attracted to your bean sprouts. Soon, when the word spreads, several more fruit flies may gather on top of your bean sprouts. In the warmer months, fruit flies tend to become a reoccurring and uninvited guest. Even though you cannot completely prevent them from flying over your bean sprouts, you can reduce the number of fruit flies that find their way to your home. You can create a fruit fly trap using apple cider vinegar.