Since credit is not reflected in Form 26AS, looks like the employer has not paid the tax to dept according to clause 1A of section 192. If non-deduction was the case, he would have been treated as assessee in default and
1. Interest will be charged under clause (1A) of section 201 and,
2. Penalty u/s 221 will be charged and,
3. Penalty u/s 271C will be charged( but only by Jt. commissioner). But this is not the case.
Here, he didn't pay to department and he will be treated as assessee-in-default, and the terms are:
1. Interest will be charged under clause (1A) of section 201 and,
2. Penalty u/s 221 will be charged and,
3. Prosecution u/s 276B will be started
So, all responsibility is with the tax deducter and the contractor/employee don't have to worry. The TDS Certificate u/s 203 (Form 16 in this case) will be sufficient to prove before the assessing officer. But if you got time, I suggest taking up the matter with the deductor- to know if any fraud is going on.