How to make wp_enqueue_style and wp_enqueue_script work only on custom post type

You can use conditionals:

<?php
add_action( 'wp_enqueue_scripts', 'wpse_enqueues' );
function wpse_enqueues() {
    // Only enqueue on specified single CPTs
    if( is_singular( array( 'anime', 'manga' ) ) ) {
        wp_enqueue_style( 'wp-manga-plugin-css', WP_MANGA_URI . 'assets/css/style.css' );
    }
}
?>

If you need the CSS on archives as well, that’s another condition:

if( is_singular( array( 'anime', 'manga' ) ) || is_post_type_archive( array( 'anime, 'manga' ) ) ) {
    wp_enqueue_style( 'wp-manga-plugin-css', WP_MANGA_URI . 'assets/css/style.css' 
}