Custom Pagination is Broken

Chances are your pager is getting the count of all posts, regardless of whether they are published. In your query, you should add a filter for only published posts.

    $query_args = array(
        'post_type' => 'post',
        'posts_per_page' => 4,
        'paged' => $paged,
        'post_status' = 'publish', 
    );

Then the results count and number of pager links should match what you actually see rendered.