Buddypress follow conflict

The problem with the plugin is it is querying for posts on the 'pre_get_posts' hook, so this means that this plugin will run code that runs on the main post hooks twice.

Since it looks like this plugin is only meant to be looking for already-queried posts, I would recommend rewriting the mark_posts_as_read() method to the following:

public function mark_posts_as_read($posts, $query) {
    $headers = function_exists('getallheaders') ? getallheaders() : $this->get_headers();
    if ($headers && isset($headers['X-Moz']) && $headers['X-Moz'] === 'prefetch') return $posts;
    if ($this->posts_marked || $this->is_special_page() || ! $query->is_main_query()) return $posts;
    $this->posts_marked = true;
    $read_posts_ids = $this->get_read_posts_ids();
    $update_cookie = false;
    foreach ($posts as $post) {
        $post_id = $post->ID;
        if ($this->is_after_cookie_time($post) && !in_array($post_id, $read_posts_ids) || $this->is_test) {
            $this->new_posts_displayed = true;
            if ($this->options->mark_after !== MarkNewPosts_MarkAfter::OPENING_POST || is_single()) {
                $read_posts_ids[] = $post_id;
                $update_cookie = true;
            }
        }
    }
    if (!$update_cookie) return $posts;
    array_unshift($read_posts_ids, $this->last_visit);
    $this->set_cookie(join(self::COOKIE_DELIMITER, $read_posts_ids));
    return $posts;
}

Then change your hook from 'pre_get_posts' to 'the_posts':

add_filter('the_posts', array(&$this, 'mark_posts_as_read'), 10, 2);

I’m not 100% sure if this will break certain parts of your plugin, but hopefully it gives you an idea of where to optimize your code.