Do not parse shortcode in CPT

I believe you need something like this-

add_filter( 'the_content', 'wpse_303180_remove_shortcode' );
function wpse_303180_remove_shortcode( $content ) {
    global $post;
    if( get_post_type( $post ) == 'my-cpt' ) {
        remove_shortcode( 'my-custom-shortcode' );
        // remove_all_shortcodes(); // to remove all shortcodes
    }

    return $content;
}