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I have created a cpt like this:

 register_post_type( 'mission', array(
    'labels'              => array( ... ),
    'supports'            => array( 'title', 'editor', 'comments', 'revisions', 'trackbacks', 'author', 'post-formats' ),
    'taxonomies'          => array( 'mission_category', 'mission_client', 'mission_location', 'mission_status'), 
    'hierarchical'        => false,
    'public'              => true,
    'show_ui'             => true,
    'show_in_menu'        => true,
    'show_in_nav_menus'   => true,
    'show_in_admin_bar'   => true,
    'menu_position'       => 5,
    'menu_icon'           => 'dashicons-star-filled',
    'can_export'          => true,
    'has_archive'         => true,
    'exclude_from_search' => false,
    'publicly_queryable'  => true,
    'capability_type'     => 'post', 
    ) 
);

and a custom taxonomy for the cpt above:

 register_taxonomy( 'mission_category', array( 'mission' ), array(
    'public'            => true,
    'show_ui'           => true,
    'show_in_menu'      => true,
    'show_in_nav_menus' => true,
    'show_tagcloud'     => true,
    'show_admin_column' => true,
    'hierarchical'      => true,
    'capabilities' => array(
        'manage_terms' => 'manage_categories',
        'edit_terms'   => 'manage_categories',
        'delete_terms' => 'manage_categories',
        'assign_terms' => 'edit_posts',
        ),
    'rewrite' => array(
        'slug'         => 'mission/category',
        'with_front'   => false,
        'hierarchical' => true,
        'ep_mask'      => EP_NONE
        ),
    )
);

I have created two mission_categories named: "Engineering" and "Economy". I expect to find an archive pages at these endpoints: /mission/category/engineering and /mission/category/economy

I also have created two pages with the same name as the categories above. I expect to find these pages at: /engineering and /economy

The strange thing is that when I hace created pages with the same name as my mission_categories, I get redirected to the page when trying to view an archive. That means, if I manually enter this endpoint /mission/category/economy i end up at /economy. Worth mentioning is that the "view-link" from the mission_category page in the admin are correct, but I still get redirected to the page when clicking on it.

This only happens when I have a page with the same name as a category... If I for example remove the economy page, the /mission/category/economy ends up at the correct url.

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I found a solution to this by some extensive googling. The key is to declare the taxanomy before the ctp. I have no idea why, but it works =)

source: https://cnpagency.com/blog/the-right-way-to-do-wordpress-custom-taxonomy-rewrites/

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