Learndash Yoast Breadcrumbs

funtions.php

add_filter( 'wpseo_breadcrumb_links', 'wpse_100012_override_yoast_breadcrumb_trail' );

function wpse_100012_override_yoast_breadcrumb_trail( $links ) {
    global $post;

    if ( is_singular( 'sfwd-lessons' ) ) {

        $course_id = learndash_get_course_id($id);
        $course_title = get_the_title($course_id);

        $breadcrumb[] = array(
            'url' => get_post_type_archive_link( 'sfwd-courses' ),
            'text' => 'Courses',
        );

        $breadcrumb[] = array(
            'url' => get_permalink( $course_id ),
            'text' => $course_title,
        );

        array_splice( $links, 1, -2, $breadcrumb );
    }

    if ( is_singular( 'sfwd-topic' ) ) {

        $course_id = learndash_get_course_id($id);
        $course_title = get_the_title($course_id);

        $parent_lesson_id = learndash_get_setting( $post, 'lesson' );

        $lesson_title = get_the_title($parent_lesson_id);

        $breadcrumb[] = array(
            'url' => get_post_type_archive_link( 'sfwd-courses' ),
            'text' => 'Courses',
        );
        
        $breadcrumb[] = array(
            'url' => get_permalink( $course_id ),
            'text' => $course_title,
        );

        $breadcrumb[] = array(
          'url' => get_permalink( $parent_lesson_id ),
          'text' => $lesson_title,
        );

        array_splice( $links, 1, -2, $breadcrumb );
    }

    return $links;
}

You can read how this code works on my website here - https://www.diviframework.com/topic/breadcrumb-learndash-snippet/