The first thing that I would do is send out a letter informing them of the overpayment and requesting that they pay back the overpayment voluntarily. I would even go so far as offering to allow them to pay it back in installments if the overpaid amount is significant. In the letter, you should state the specific amount that was overpaid, what caused the overpayment to happen, and lay out the terms under which they can pay it back. If they consent, then you can deduct it from their paychecks, but only if they consent and if the amount is significant, again, you would want to allow them to have a payment schedule.
For those employees that do not pay the overpayment back, you can hire a law firm to send them official letters to recover the money. You can also sue them in court but I would consider that as a last resort only. You will have to make the decision of whether it is worth it financially to you to hire a law firm/debt collector to do this.
To make things even more complicated, the recovery methods available to you will depend on whether the employees were exempt or nonexempt because of FLSA
law. Many courts have ruled that if you overpay exempt employees, you are basically out of luck.
The other thing that you need to be aware of is that you will need to correct payroll
records for IRS purposes for these employees and, depending on the tax year that the repayments are made, you should also notify your employees of the tax implications.