WordPress automatically adds the current-menu- class to any navigation link that links to the current page.
So ALL those links are current, and current link styles best hover styles. To correct that you will need CSS:
.header-wrap #site-navigation:not(.toggled) .main-nav > ul > li[class*="current-menu-"]:hover > a {
background: rgba(241,196,15,0);
color: #f1c40f;
}