From WordPress 3.0 version we are able to use the custom_post_type. In installation time of theme or plugin new permalink structure will be created and you can easily able to use the custom post type permalink.
If your custom_post_type function is having some issues then wordpress permalink for your custom post type will not work. If your custom post type permalink is not working properly then normally you will get the 404 page and message saying page not found.
Your wordpress does not create the permalink structure aumatically so you need to recreate the Rewrite rules again with wordpress.
If you not added following code in you custom_post_type function then please add the following code:
'rewrite' => array( 'slug' => 'issue', 'with_front' => FALSE, ),
The right way to use rewrite rule in function is as follows;
register_post_type( 'movies', array( 'label' => __('Movies') , 'public' => true, 'show_ui' => true , 'rewrite' => array( 'slug' => 'movies', 'with_front' => false ) ) );
If you are still facing issue and 404 page is coming then go the your wordpress panel -> setting- > permalink page and hit save changes button.
That will flushes the rewrite rules and build rewirte rules again in wordpress.