.Have you completed and submitted your tax return online? I suspect that you haven't chosen to offset the loss from self-employment against your salary which will result in you being overpaid. A quick way to find out is to view your tax return and see if the loss appears in either box 33 here or in box 78 here.
Find the box in the self-employment section of the online tax return to offset the loss against other income /14 and put the loss in there. That should have the desired effect.
I hope this helps but let me know if you have any further questions.
Thanks Tony, all sorted & that made a big difference!