Add filter Wordpress (Shortcode not working in rss)

I've replaced the default Wordpress gallery with an custom plugin using BxSlider.

The plugin is working as it should on the front end.

<?php
/*
Plugin Name: Weemsel Gallerij
Plugin URI: http://ift.tt/21jIYuz
Description: Weemsel Gallerij met Facebook instant articles support
Version: 1.0
Author: Het Weemsel
Author URI: http://ift.tt/21jIYuz
*/

remove_shortcode('gallery');
add_shortcode('gallery', 'parse_gallery_shortcode');

wp_register_style('bxslider-css', plugins_url() . '/weemsel-gallerij/assets/css/jquery.bxslider.css', false, null);
wp_enqueue_style('bxslider-css');

wp_register_script('bxslider-js', plugins_url() . '/weemsel-gallerij/assets/js/jquery.bxslider.min.js', false, null, true);
wp_enqueue_script('bxslider-js');

wp_register_script('setup-js', plugins_url() . '/weemsel-gallerij/assets/js/bxsetup.js', false, null, true);
wp_enqueue_script('setup-js');  

function parse_gallery_shortcode($args) {

    global $post;

    if ( ! empty( $atts['ids'] ) ) {
        // 'ids' is explicitly ordered, unless you specify otherwise.
        if ( empty( $atts['orderby'] ) )
            $atts['orderby'] = 'post__in';
        $atts['include'] = $atts['ids'];
    }

    extract(shortcode_atts(array(
        'orderby' => 'menu_order ASC, ID ASC',
        'include' => '',
        'id' => $post->ID,
        'itemtag' => 'dl',
        'icontag' => 'dt',
        'captiontag' => 'dd',
        'columns' => 3,
        'size' => 'full',
        'link' => 'file'
    ), $atts));


    $args = array(
        'post_type' => 'attachment',
        'post_status' => 'inherit',
        'post_mime_type' => 'image',
        'orderby' => $orderby
    );

    if ( !empty($include) )
        $args['include'] = $include;
    else {
        $args['post_parent'] = $id;
        $args['numberposts'] = -1;
    }

    $images = get_posts($args);
    ?>
    <?php
    ob_start();

        echo '<ul class="bxslider">';
            foreach ( $images as $image ) { 
                    echo '<li><figure><img src="';
                    echo wp_get_attachment_url($image->ID, $size);
                    echo '" /></figure></li>';
                }
        echo '</ul>';




        echo '<div id="bx-pager">';

            $i = 0;

            foreach ( $images as $image ) { 
                    echo '<a data-slide-index="';
                    echo $i++;
                    echo $item[number];
                    echo '" href=""><figure><img src="';
                        echo wp_get_attachment_image_url($image->ID, $size);
                    echo '" /></figure></a>';           
            }
        echo '</div>';


    $content = ob_get_contents();
    ob_end_clean(); 

    return $content;

}

add_filter('the_excerpt','do_shortcode', 10, 100);
add_filter('the_content','do_shortcode', 10, 100);
add_filter('the_excerpt_rss','do_shortcode', 10, 100);
add_filter('the_content_rss','do_shortcode', 10, 100);
?> 

Somehow when using the add_filter function the outcome in RSS is really weird not outputting the html nor the correct links. The RSS feed is a custom made feed

<?php
/**
 * Template Name: Zakelijke feed
 */
$postCount = 5; // The number of posts to show in the feed
$posts = query_posts('showposts=' . $postCount .'&cat=52');
header('Content-Type: '.feed_content_type('rss-http').'; charset='.get_option('blog_charset'), true);
echo '<?xml version="1.0" encoding="'.get_option('blog_charset').'"?'.'>';
?>
<rss version="2.0"
        xmlns:content="http://ift.tt/yb6HFH"
        xmlns:wfw="http://ift.tt/xYRqlD"
        xmlns:dc="http://ift.tt/mToXri"
        xmlns:atom="http://ift.tt/r5ut6F"
        xmlns:sy="http://ift.tt/wvwGq0"
        xmlns:slash="http://ift.tt/y8Ql4d"
        <?php do_action('rss2_ns'); ?>>
<channel>
        <title><?php bloginfo_rss('name'); ?> - Feed</title>
        <atom:link href="<?php self_link(); ?>" rel="self" type="application/rss+xml" />
        <link><?php bloginfo_rss('url') ?></link>
        <description><?php bloginfo_rss('description') ?></description>
        <lastBuildDate><?php echo mysql2date('D, d M Y H:i:s +0000', get_lastpostmodified('GMT'), false); ?></lastBuildDate>
        <sy:updatePeriod><?php echo apply_filters( 'rss_update_period', 'hourly' ); ?></sy:updatePeriod>
        <sy:updateFrequency><?php echo apply_filters( 'rss_update_frequency', '1' ); ?></sy:updateFrequency>
        <?php do_action('rss2_head'); ?>
        <?php while(have_posts()) : the_post(); ?>
                <item>
                        <title><?php the_title_rss(); ?></title>
                        <link><?php the_permalink_rss(); ?></link>
                        <pubDate><?php echo mysql2date('D, d M Y H:i:s +0000', get_post_time('Y-m-d H:i:s', true), false); ?></pubDate>
                        <dc:creator><?php the_author(); ?></dc:creator>
                        <guid isPermaLink="false"><?php the_guid(); ?></guid>
                        <description xml:space="preserve"><![CDATA[ <?php the_post_thumbnail( 'medium' );  ?> ]]><![CDATA[ <?php the_excerpt(); ?> ]]></description>
                        <content:encoded xml:space="preserve"><![CDATA[ <?php the_post_thumbnail(); ?> ]]><![CDATA[ <?php the_content_rss() ?> ]]></content:encoded>
                        <?php rss_enclosure(); ?>
                        <?php do_action('rss2_item'); ?>
                </item>
        <?php endwhile; ?>
</channel>
</rss>

The output i'm getting is really weird and can be seen at the following url: http://ift.tt/21jHkcq

https://woerden.tv"><figure><img src= [3] https://woerden.tv"><figure><img src= [4] https://woerden.tv"><figure><img src= [5] https://woerden.tv"><figure><img src= [6] https://woerden.tv"><figure><img src=

Anyone who can tell me what's going wrong?

Best Regards, Dylan

via Chebli Mohamed