[wp-invoice] shortcode shouldn't show any invoice by itself. It only shows the place on the page where should be your invoice and only if you have this option enabled.
So if you included shortcode [wp-invoice] in the content of the page, users will see just shortcode, not invoice on this page, so be sure users do not have direct link to this page.
When you will send particular invoice to someone from your site, they will see their invoice page you set up.
You can use another method how to insert invoice to the page so you won't need shortcode at all.