Set Yoast PRIMARY category as the peralink

yoast-primary-category-permalinks.php

// FIX PERMALINK OF CATEGORIES MATCHING PRIMARY CATEGORY
add_filter( 'wc_product_post_type_link_product_cat', function( $term, $terms, $post ) {

    // Get the primary term as saved by Yoast
    $primary_cat_id = get_post_meta( $post->ID, '_yoast_wpseo_primary_product_cat', true );

    // If there is a primary and it's not currently chosen as primary
    if ( $primary_cat_id && $term->term_id != $primary_cat_id ) {

        // Find the primary term in the term list
        foreach ( $terms as $term_key => $term_object ) {

            if ( $term_object->term_id == $primary_cat_id ) {
                // Return this as the primary term
                $term = $terms[ $term_key ];
                break;
            }

        }

    }

    return $term;

}, 10, 3 );

Source: https://wordpress.org/support/topic/same-product-under-multiple-categories-wrong-permalink/#post-11535196