HMRC have published guidance for employers on what to do if they have been reporting payments to employees in real time which do not match with the actual date of payment or with tax periods.
When you report your PAYE in real time, your Full Payment Submission (FPS) must report the correct payment date. This being the date on which your employees were paid. This is not the date that the payroll is run unless the date is the same as payment.
More details are available from HMRC