It is the responsibility of the employer to deduct tax properly and remit the same to the Government. In the case of short deduction, he can make it good and remit the same along with interest. However, it may create a problem if you have already filed your return. If you have not filed the return, then he can remit the short deduction and issue Form No. 16 afresh. There is penalty only on the employer and not on the employee. However, if there is reasonable cause for such short deduction, penalty may not be levied.