To reduce income tax fraud the IRS is mandated to verify wages you entered against the information the employer provides ... this one action saves the US taxpayers billions is fraudulent refund payments.
Back in the days when the return was mailed in you attached the W-2 form to the return and the income you entered was verified on the spot ... now with electronic filing the IRS has to do it thru the system and sometimes the employer's information takes longer to get in the system (especially if they still mail in the forms) so the verification takes longer.
I had a client who worked for a small firm, only 7 employees, and they mailed in the forms and the data input operator missed scanning in her form and it took more than 4 months for them to track down the error. All you can do is be patient in these cases while they work themselves out.
