I created an invoice but did not send it about 2 weeks ago, when I completed the job I went back to the invoice only to find that quick books had marked it as paid.

Hello Alecmorrow, 

Welcome to the Community page, 

If you have matched the invoice to the payment on the banking page then it will automatically apply the payment for you so that will be by when you have then gone into the invoice it shows as paid for you.