Q: We have realised that we have been overpaying an employee in the Czech Republic for a few months now.  Can we claim the money back?  Can we simply proceed with deductions?

It is not possible to proceed with any deduction from wages without first informing the employee.  It is necessary to discuss the matter with the employee, state your case clearly and construct a repayment plan so that repayments are not overly burdensome for the employee.  The specific issue requires careful handling considering facts on a case to case basis. It is not wise to accuse the employee of being aware of the overpayment as this will reduce readiness to cooperate.