How can we avoid W-2 glitches?

Question: On last year’s W-2s, Accuwage flagged a Social Security number (SSN) beginning with a nine. We called the Social Security Administration (SSA) and were advised to enter nine zeros for this SSN. We later learned that the SSN was an Individual Taxpayer Identification Number (ITIN). Should we have reported the nine zeros or the ITIN, even though the W-2 instructions say not to accept an ITIN from an employee?