This explains what to do when allocating CIS invoices and credit notes together that don't match.
When this happens we show you a mismatch error.
You can continue to allocate in these scenarios. However, there are workarounds to help you to resolve them.
How this works
We show you a mismatch error when:

We only show CIS deductions as paid on your monthly CIS return when you match the invoices to a payment.
When you allocate a credit note this does not affect the monthly return as you have not received a payment.
Where both the invoice and the credit note have CIS deductions, this is not a problem. The CIS withheld amounts offset each other.
When a credit note has no CIS deduction, there is no offsetting of the CIS amount. It remains outstanding and shows on the CIS withheld ledger account.
This explains what to do if:
You still need to 'pay' the CIS withheld amount. Make sure it is on your monthly return.
We recommend that you:
In our example, we have a CIS invoice for £100. The withheld amount is £30. This leaves an outstanding balance of £70. You don't need to pay £70 to the subcontractor and wait for the subcontractor send a refund. Allocate £70 from a non-CIS credit note to pay off the balance.
To do this:
This shows the CIS withheld as paid and includes it on your monthly return.
In our example, we make a payment of £70. Although no actual money changes hands, £70 shows against the bank account. The CIS monthly return now reports the £30 CIS amount.
This should be for the same amount you paid against the invoice. The payment you just made cancels out.
In our example, we refund £70 against the credit note. The refund also shows on your bank account but cancels out the payment made against the invoice.
The deduction rate may change between recording an invoice and recording the credit note. You will see a mismatch error when allocating the two together.
This could happen when a subcontractor issues a CIS invoice with a 20% deduction rate. The contractor could be missing important information such as the UTR. Or the HMRC couldn't find the UTR on the list of registered subcontractors. In this circumstance, HMRC require that the contractor pays the subcontractor at the 30% deduction rate.
Both parties can easily resolve this:
As the contractor:
The subcontractor:
In this scenario, don't try to allocate between a stand alone CIS credit note and CIS invoice with different CIS labour amounts. Arrange to refund the stand alone CIS credit note. Add a credit note to the outstanding CIS invoice.
This ensures your accounts remain accurate and ensures the correct reporting of your CIS payments.