Pagination calling 404.php

Hi,
Im coming with a new issue!

I have an index.php with 4 differents and a pagination.
To have my pagination works i hade to find a way to not use the offset option.

So there is my index.php:

<?php GET_HEADER(); ?>
     <section class="first-news flex inner">
<?php

/**
 **
 ** The first loop that show the first 2 post
 **
 **
 */

query_posts(array('ignore_sticky_posts' => 1, 'showposts' => 2));
$ids = array();
while (have_posts()) : the_post();
$ids[] = get_the_ID();  ?>   

      <article class="flex-6">
        <a href="<?php the_permalink() ?>">
          <?php the_post_thumbnail( 'thumbnail_top2' ); ?>
          <div class="db-border"></div>
          <div class="overlay">
            <div class="overlay-inner">
              <h2 class="white"><?php the_title(); ?></h2>
              <div class="cat dessert">Dessert</div>
            </div>
          </div>
        </a>
      </article>
<?php endwhile;  ?>  

/**
 **
 ** The second loop that ignore the first 2 post and show the next 3 posts
 **
 **
 */

<?php
query_posts(array('ignore_sticky_posts' => 1, 'post__not_in' => $ids, 'showposts' => 3));
while (have_posts()) : the_post();
$ids[] = get_the_ID();
  ?>
      <article class="flex-4">
        <a href="<?php the_permalink() ?>">
          <?php the_post_thumbnail( 'thumbnail_nextTop3' ); ?>
          <div class="db-border"></div>
          <div class="overlay">
            <div class="overlay-inner">
              <h2 class="white"><?php the_title(); ?></h2>
              <div class="cat dessert">Dessert</div>
            </div>
          </div>
        </a>
      </article>
<?php endwhile;?>     

    </section>
    <div class="separation" id="last-news"><h1>Il y a encore pleeeein de recette par ici!</h1></div>

    <div class="flex inner">
      <section class="flex-9 last-news">
        <div class="content flex">     

/**
 **
 ** the third loop that display the 9next posts
 **
 **
 */

<?php
  global $wp_query;
  $temp = $wp_query;
  $wp_query = new WP_Query();
  $wp_query->query('posts_per_page=9'.'&paged='.$paged);
  query_posts(array('ignore_sticky_posts' => 1, 'post__not_in' => $ids,'showposts' => 9, 'paged' => $paged));
      while (have_posts()) : the_post(); ?>       

        <article class="flex-4">
         <a href="<?php the_permalink() ?>">
            <?php the_post_thumbnail( 'thumbnail_nextTop3' ); ?>
            <div class="comment"><span class="number"><?php comments_number('0','1','%'); ?></span><i class="fa fa-comment"></i></div>
            <div class="desc">
              <div class="cat boisson">boisson</div>
              <h2><?php the_title(); ?></h2>
              <p><?php the_excerpt(); ?></p>
            </div>
          </a>
        </article>
       <?php endwhile; ?>

/**
 **
 ** there is my pagination
 **
 **
 */

  <?php
    pressPagination($pages ='', $range = 2) ;
    $wp_query = null;
    $wp_query = $temp;
  ?>
        </div>
      </section>

<?php GET_SIDEBAR(); ?>

      </div>
      <section class="pop inner">
        <h5>Les articles les plus populaires</h5>
        <div class="flex">
/**
 **
 ** And there is a fourth loop to display the most valuable posts according to the number of their comments
 **
 **
 */

<?php query_posts(	array('ignore_sticky_posts' => 1, 'posts_per_page' => 4, 'orderby' => 'comment_count', 'order' => 'DESC')); ?>
	<?php while (have_posts()) : the_post(); ?>
	          <article class="flex-6 flex align-center">
            <div class="flex-4"><a href="<?php the_permalink() ?>"><?php the_post_thumbnail( 'thumbnail_pop' ); ?></a></div>
            <div class="flex-8">
              <h2><?php the_title(); ?></h2>
              <?php the_advanced_excerpt('length=40&length_type=words&no_custom=1&ellipsis=%26hellip;'); ?>
              <footer class="ovh flex align-center">
                <div class="left comment flex-6"><a href="#"><?php comments_number('0','% commentaire','% commentaires'); ?></a></div>
                <div class="flex-6"><a href="<?php the_permalink() ?>" class="btn right" >Lire l'article</a></div>
              </footer>
            </div>
          </article>
	<?php endwhile;?>
        </div>      

      </section>
<?php GET_FOOTER(); ?>

There is the code in functions.php for the pagination

// Pagination
function pressPagination($pages = '', $range = 2)
{
    global $paged;
    $showitems= ($range * 2)+1;

    if(empty($paged)) $paged = 1;
    if($pages == '')
    {
        global $wp_query;
        $pages = $wp_query->max_num_pages;
        if(!$pages)
        {
                   $pages = 1;
        }
    }

    if(1 != $pages)
    {
        echo "<ul class='pagination flex-12 center inline inner' data-load='pagination'>";
        if($paged > 2 && $paged > $range+1 && $showitems < $pages) echo "<li><a href='".get_pagenum_link(1)."'>«</a></li>";
        if($paged > 1 && $showitems < $pages) echo "<li><a href='".get_pagenum_link($paged - 1)."'>‹</a></li>";

        for ($i=1; $i <= $pages; $i++)
        {
            if (1 != $pages &&( !($i >= $paged+$range+1 || $i <= $paged-$range-1) || $pages <= $showitems ))
            {
                echo ($paged == $i)? "<li><span class='current'>".$i."</span></li>":"<li><a href='".get_pagenum_link($i)."' class='inactive' >".$i."</a></li>";
            }
        }

        if ($paged < $pages && $showitems < $pages) echo "<li><a href='".get_pagenum_link($paged + 1)."'>›</a></li>";
           if ($paged < $pages-1 &&  $paged+$range-1 < $pages && $showitems < $pages) echo "<li><a href='".get_pagenum_link($pages)."'>»</a></li>";
           echo "</ul>";
       }

}

Everything is working fine this way BUT when i create my 404.php file, the last 3 pages of my pagination goes this way! But if i don’t have any 404.php file, the last 3 pages works fine!

what can goes wrong? 🙁

Thanks for your time