According to Illumiseen, those extra holes can actually serve an important purpose. They can help make shoes fit better, and thus prevent blisters by creating a lace or heel lock.
The idea of the “lace lock” is not new, but it’s still creating quite the buzz for those not up to par with this basic technology.
This method creates just enough friction between the laces at your ankle, thus keeping your toes from jamming into the front of the shoe and keeps the foot tightly seated for a more comfortable wearing experience.
This handy little trick also works on shoes that don't have the extra hole. In that case, you can just use the standard top hole to tie the loop lock. Try it in your hiking boots, your climbing shoes, or any pair of laced shoes that can use a little extra snugness. Remember to make sure that your laces are snug and not overtightened, which can make for a high unpleasant running or walking experience.