Order processed but remained in Cart. Why?

I had a client process an order and submit payment via paypal. I know the order was paid for by the email I got from paypal. However, when I go to the database and inspect it, it shows that order still in the shopping cart of the user. Is there any way to move the order to a closed state via the admin or another way? And, is there a cause that anyone knows about for this to happen?

Your assistance appreciated.