In fact, don't you think the boss should take action against HR for paying out with incomplete punch cards? About the return of punch card, it is one person's words against another person's. Anyway, about deduction, section 24(2) of the Employment Act may provide the info:
"(2) It shall be lawful for an employer to make the following deductions—
(a) deductions to the extent of any overpayment of wages made during the immediately preceding three months from the month in which deductions are to be made, by the employer to the employee by the employer’s mistake; "
Now, it is difficult to say who is right and who is wrong. Consult the Labour Department by giving them a call and get some official advice.