How may I approach this ETL logic?

I have three pkgs.

Organization (runs first)

Department (runs second)

Employee(runs third)

Source file for Organization will have OrganizationID + DepartmentID + EmployeeID + ErrorFlag

i.e. 1 1 1

now, DepartmentID and EmployeeID cannot repeat for another OrganizationID

i.e. 1st record = 1 1 1 and 5th record = 4 1 1 (this cannot happen).

If that happens, I want to mark that 4 1 1 record as True for ErrorFlag column.

I want to then apply same logic for Department where 1 emp cannot be in multiple dept.

Can I get some ideas on how to approach that in ETL? I want to mark the 2nd+ instance of duplicate foreign values to True.

Thank you