posts_per_page showing 16 elements instead of 3

Your query might be picking up sticky posts. To ignore them, try this:

    $args = array(
      'meta_query' => array(
            array(
              'key' => 'featured_posts',
              'compare' => '==',
              'value' => '0'
            )
          ),
      'post_type' => 'post',
      // Changed '3' to 3, since WP_Query expects an int.
      'posts_per_page' => 3,
      // Ignore the sticky posts.
     'ignore_sticky_posts' => true,
    );