How can I pull information from my loop and divide them seperately?

You don’t put the controls in the while loop, then they will come there every time. So you can use a for loop and the found_posts variable to loop trough the items before and after the while loop.

Example below.

<div class="gallery autoplay items-3">  

    <?php
    $args = array(
        'post_type' => 'referanse'
    );
    $referanser = new WP_Query( $args );
    ?>

    <?php if( $referanser->have_posts() ) : ?>
        <?php for($i=1; $i<=$referanser->found_posts; $i++) : ?>
            <div id="item-<?php echo $i; ?>" class="control-operator"></div>   
        <?php endfor; ?>

        <?php while( $referanser->have_posts() ) : $referanser->the_post(); ?>
            <figure class="item">
                <h1><?php the_title() ?></h1>
            </figure>
        <?php endwhile; ?>

        <div class="controls">
        <?php for($i=1; $i<=$referanser->found_posts; $i++) : ?>
            <a href="#item-<?php echo $i; ?>" class="control-button">•</a>
        <?php endfor; ?>
        </div>

    <?php else : ?>
       Ops, ingen referanser enda...
    <?php endif; ?>

</div>