This is a common problem when you have an abundance of links and a fixed menu with minimum scroll available. Mega Menu have posted 2 fixes here: https://www.megamenu.com/documentation/fixed-height-mega-sub-menu/ but if that doesn’t solve the issue you can try the modified version that worked for us:
@media only screen and (min-width: 992px) {
#mega-menu-wrap-primary #mega-menu-primary > li.mega-menu-flyout ul.mega-sub-menu li.mega-menu-item ul.mega-sub-menu {
overflow-x: hidden;
height: 200px;
overflow-y: scroll;
}
}