This sounds like the same problem I had, WordPress added a home option to the menu without it being added in the appearance menu items so I could not remove it. I googled for ages and found two solutions. Neither of them worked but if I combined the two they did. Open the functions.php file in your site files. If you are using a common theme there might be a function already in there that states something like $args['show_home'] = true; if that is the case then just change the true to false and save the file.
If you are using your own theme or the current theme does not add home to menus by default then just copy the below code, paste it in functions.php, change the yourTheme to the name of your theme and save
function yourTheme_page_menu_args( $args ) {
$args['show_home'] = true;
return $args;
}
add_filter( 'wp_page_menu_args', 'yourTheme_page_menu_args' );