If your employees paid too much tax for the previous period, you may be able to get a tax rebate. The HMRC will be the one who'll pay the tax rebate, and you'll have to claim it.
After you claim it, you can then create an expense that shows this overpayment for your employee with HMRC assigned as a vendor. Here's how:
Go to the +New button.
Select Expense.
Set the Payee as HMRC.
Under the Category column, enter the liability account.
Enter the overpayment amount, and set the VAT to No VAT.
Hit Save and close.
However, since you'll need clarification on why your company would pay it, I'd recommend consulting your tax advisor for further assistance with this matter. You can also contact HMRC to verify this scenario.