Listen to Carol. The employer withheld monies from employee that shouldn't have been withheld. The employer needs to make the employee whole. Did the employer violate minimum wage laws? Did the employer fail to pay a union worker what they were entitled to? Are there contractual obligations or remedies that would apply? Whatever is required, they must do. Payroll manager should listen to attorney and do what Carol said (make employee whole, including contractual penalties, if any).
If temporary employees are not eligible for the plan, then the plan is not involved. It never received monies attributable to employee and, even if it had, since employee not entitled to have money in the plan, the plan's obligation would be to repay the plan sponsor (or to use the funds to settle up with the plan sponsor vis-a-vis other funds that are due).
I have no words to describe the payroll manager. Essentially, because of the payroll manager's incompetence an employee had a portion of their paycheck stolen by the agency and now the agency's representative is refusing to allow the agency to recognize its error and make things right! This is the sort of governmental misconduct that makes for a great story in a national magazine.
Maybe the payroll manager isn't cooperating because this is a systemic issue affecting a lot of employees. Maybe no cooperation because the funds have been embezzled by the payroll manager? Obviously, not terribly likely, but why else would the payroll manager not budge?