Permalink issues with custom taxonomies

I think that when you define custom rewrite slugs in the registration of a custom taxonomy, you still need to add custom rewrite rules.

add_action('init','my_add_rewrite_rules');
function my_add_rewrite_rules() {
    add_rewrite_rule( 'rights/category/(.+)/page/([0-9]{1,})/?$', 'index.php?post_type=rights&category=$matches[1]&paged=$matches[2]', 'top' );
    add_rewrite_rule( 'rights/category/(.+)/?$' , 'index.php?post_type=rights&category=$matches[1]' , 'top' );
}

In order to add the correct rewrite rule I would need the code of the custom post type and custom taxonomy registration. Also, don’t forget to flush rewrite rules by visiting WP admin area->settings->permalinks.

I can confirm from my own tests that @G.M. is correct (see first comment to the question). If you register your cpt with the singular name right and set the has_archive argument to the plurgal slug rights, the custom rewrite argument in register_taxonomy you are using will work without any custom rewrite rules. So you can register the cpt with register_post_type('right', $args) where $args['has_archive'] = 'rights'. But now you will have:

domain.com/rights/ -> for archive view
domain.com/right/a-custom-post/ -> for single custom post view
domain.com/rights/taxonomy-slug/term-slug/ -> the term archive view

So, I still prefer register the cutom post type with plural slug and add the rewrite rules in order to have a more consistent permalink structure like this (all urls will inclue ‘rights’ slug):

domain.com/rights/ -> for archive view
domain.com/rights/a-custom-post/ -> for single custom post view
domain.com/rights/taxonomy-slug/term-slug/ -> the term archive view

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