Hello KatL, 

Please can you reach out to us on either Twitter or Facebook and send us a DM/PM with the email address linked to your account so we can look into this more for you. The calculations in Quickbooks Self-Employed goes off the information that you have inputted into the system. When you reach out to us on either twitter or Facebook can you also let us know what figures you are using to do the manual calculations so we can look into it more for you. 

Twitter - https://twitter.com/QuickBooksUK

or 

Facebook - https://www.facebook.com/QuickBooksUK