Custom Permlinks work, regular page permalinks don't

Question

I have some custom permalinks for my custom post types, that look like so:

/products/category/subcategory/product-name

I wrote a generate_rewrite_rules function for the permalinks related to that custom post type.

However, any regular pages I create via WP's interface show up as 404s, while those custom permalinks still work. I'm convinced it's an Apache problem. Can't figure out what's wrong.

I have an editable .htaccess in place, with the normal stuff inside...

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

My apache conf file for the relevant server:

<Directory />
        Options FollowSymLinks
        AllowOverride All
</Directory>
<Directory /path/to/folder>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride All
        Require all granted
        Order allow,deny
        allow from all
</Directory>

EDIT Running WP 4.8.1, on Ubuntu 14.04

EDIT 2: Just noticed this is a WP 404, not an apache 404. So this is down to my rewrite rules, and I've noticed that the rewrite is looking for every page being one of my custom taxonomy, as in (index.php?product-category=$matches[1]) and that's why I get the 404. Of course this shouldn't happen.

How do I fix it? My function is a bit of a nest.

function custom_rewrite_rules($wp_rewrite) {
    $newRules = array();
    $terms = get_terms( array(
        'taxonomy' => 'product-category',
        'hide_empty' => false,
    ) );

    foreach ($terms as $term) {   
        $post_query = new WP_Query( array(
            'post_type' => 'custom_product',
            'posts_per_page' => -1,
            'tax_query' => array(
                array(
                    'taxonomy' => 'product-category',
                    'field'    => 'slug',
                    'terms'    => $term->slug,
                    'include_children' => false
                ),
            )
        )); 
        if ( $post_query->have_posts() ) : while ( $post_query->have_posts() ) : $post_query->the_post();
            if($term->parent){
                $parent = get_term( $term->parent, 'product-category');
                $newRules['products/' . $parent->name . '/' . $term->name . '/'. get_post_field( 'post_name', get_the_ID() ) . '$'] = 'index.php?taxonomy=product-category&post_type=custom_product&product-category='.$parent->slug.'&product-category='.$term->slug.'&custom_product='. get_post_field( 'post_name', get_the_ID() );
            } else {
                $newRules['products/' . $term->name . '/'. get_post_field( 'post_name', get_the_ID() ) . '$'] = 'index.php?taxonomy=product-category&post_type=custom_product&product-category='.$term->slug.'&custom_product='.get_post_field( 'post_name', get_the_ID() );
            }     

        endwhile;
        endif;
        if($term->parent){
            $parent = get_term( $term->parent, 'product-category');
            $newRules['products/' . $parent->name . '/' . $term->name . '$'] = 'index.php?taxonomy=product-category&product-category='.$parent->slug.'&product-category='.$term->slug;
        } else {
            $newRules['products/' . $term->name . '$'] = 'index.php?taxonomy=product-category&product-category='.$term->slug;
        }     
    }
    $newRules['products/(.+)/(.+)/?$'] = 'index.php?post_type=custom_product&custom_product=$matches[2]';
    $newRules['products$'] = 'index.php?post-type=page&pagename=product-categories';

    $wp_rewrite->rules = $newRules + $wp_rewrite->rules;
}

Answer 1

Most likely, you have created custom permalinks that are in conflict with default WP permalinks. Unfortunately, WP doesn't validate permalinks rules, and it is very easy to create conflicted permalinks rules.

Rules have priority hierarchy, and when resolving any request, WordPress goes through the list of rules, until it matches first one. It is possible that you have created rule that has overridden the default rule so that normal pages depending on that rule can't be resolved anymore.

You need to be very careful with permalinks rule, especially not to replace default rules without suitable replacement.