I e filed it through turbo tax. The IRS automatic system kept telling me it was processing. I called the IRS and was told that one of the two W-2 had the same EIN number. That I need to file a 1040X to correct the mistake.
First you should NEVER amend a return that has not been fully processed by the IRS yet ... the IRS really should send you a letter requiring you to mail in the W2 forms to clarify the error however this is usually an issue they will correct for you automatically but it will take time ... I would call again and get more definitive instructions.