"IT" being HTML and your browser,; and the "extra scroll bar" being only the browser scrollbar (nothing "extra")
Your site is basically a 100vh section so it never shows a scroll bar. When you activate the menu, for a reason you may find, the site suddenly gets higher than the browser height, so the browser displays a scroll bar.
Disabling the scroll bar is easy for Webkit (chrome, safari) but not for other browsers. You can read more about it here: http://stackoverflow.com/questions/16670931/hide-scroll-bar-but-still-being-able-to-scroll