If you have physcially overpaid the employee, you need to work out the net overpayment that the employee has received.
You should then speak with them and arrange to have the money repaid.
Once they have arranged to pay this back or you have received the money, you should then amend the FPS already submitted to show that the lower amount was actually paid.
Once the amended FPS have been recieved by HMRC, any overpaid tax and NIC, would sit as a credit on the employers account to which you can either request the refund or you can use to offset against future liabilities.
This is why it is important that the employee pays back the NET overpayment.
As long as this guidance was followed, there should be no issues with your account.
Guidance on Overpayment of Wages/Salary can be found on CWG2 section 1.19:
022 to 2023: Employer further guide to PAYE and National Insurance contributions
Unfortunately, I am unable to look into your account via the forum.
You will need to contact the Employers Helpline on 0300 200 3200 or by webchat here:
Employers: general enquiries
An adviser can then check your year to date totals and make sure they match your payroll software.