EPR (P32) report reconciles pay data based on "PAYMENT DATE" as per HMRC stipulation. Whereas Monthly Consolidated Cost (MCC) report and all other reports show/consolidate pay data based on the "PAY PERIOD END DATE" - which is displayed on payslips and is also known as "Process Date".
A mismatch in EPR data and MCC data will occur during pay reconciliation process when the process date is advanced to the previous pay period.
For example, when you process pay for pay period 9 ('05/12/2014' to '06/01/2015') if any of your employees, payment date for pay period 9 is advanced to '03/12/2014', so the period 9 amounts (PAYE, NIC) are included in tax month 8 of EPR itself. Due to this reason, the differences in PAYE, Employee & Employer NIC will prevail. You can cross-check by comparing the MCC report with EPR of Month 8 then you can see the PAYE / NIC differences accounted for the previous tax month (8) itself.
You can download Employee Pay Data CSV and use it for reconciliation.In this report you will have all the information you need to compare & cross-check with EPR - Payment Date & Process Date (Pay Period End Date) & Employer Payment Record ( EPR ) Month.
Follow the road map mentioned below to download Employee Pay Data CSV.
Reports -> Employee Details -> Employee Pay Data Report CSV -> Previous Year Report -> Select tax period and tax year -> Export CSV