Your employer is legally entitled to recover any overpayment of wages, both during the currency of your contract of employment, as well as after your contract has ended.
How your employer can recover an overpayment
Your employer does not need your permission to recover the overpayment of wages by way of a direct deduction from your salary, nor to necessarily notify you, unless there is express provision within the your contract of employment to do so.
By law, the employer can recover an overpayment from your wages in full, from one single pay packet, unless, again, the contract provides otherwise.
As a matter of good practice, however, even in the absence of any express contractual provision, your employer should notify you prior to making any deductions and if necessary, to try to negotiate a repayment plan with you.
When your employer recover an overpayment after your contract has ended
Having identified an overpayment post-termination, your employer will need to request repayment from you. This should be done informally at first, albeit in writing.
It is always advisable for your employer to seek to negotiate a flexible repayment plan, ensuring that some or all of the overpayment is recovered on an agreed basis.
Your employer can pursue the matter through the courts in the event that you breach any agreement.
However your employer will not be entitled to recover any overpayment of wages made more than six years ago.