To show that you know something about the Employment Act, you may look at it at two situations:
Situation #1. The employee is not covered by the Employment Act because he is a non manual employee with salary more than RM1500. In such a situation, Section 24 does not apply and the employer can make the deductions according to what were stated in the contract. Disputes may be dealt with in the civil courts.
Situation #2. Lets take the employee as a manual worker say a bulldozer driver earning RM6200 per month so that he is covered by the EA. So, in this case, Section 24 about salary deductions is clear and you can examine the clauses one by one whether the deductions were done accordingly. Should there be disputes, the employee concerned can seek redress at the Labour Department.
I can't comment on the agreement on the eduction programme sponsorship for post graduate studies. Consult a lawyer friend of yours.