The issue is with the login module at the top which doesn't redirect back to the checkout after the login.
So you think that you lost your cart, and try to add the product again in the cart, but you already have the product in the cart and thus you try to add a second product in the cart. However, you apparently have limitations to avoid a user to add more than one product in the cart and thus it displays that message and doesn't allow you to add the product again.
The normal Joomla login module redirects back to the same page by default. Isn't there a way to have a similar behavior for your login module ?