My wife has this exact situation as well...
However, I was able to get both W-2s into TurboTax even though they had the same EIN, but it tells me that she overpaid Social Security and she needs to get a W-2c from her employer and we shouldn't file without a corrected W-2c.
Under the "What if my employer won't give me a W-2c?", it states that I need to contact 1-800-TAX-1040 and the IRS will contact your employer to request it.
Under the "How much should my employer withhold?", it states that we can file IRS Form 843, Claim for Refund and Request for Abatement. This is a separate form that you can get from the IRS site and it should not be included with your tax return.
This is just all awkward and it is unclear whether I should proceed to file or not...
I presume I should do the following:
1. Have her request a W-2c from her employer
2. If the employer won't provide a W-2c, call 1-800-TAX-1040
3. If that doesn't generate a W-2c in time, just file what I have and then submit form IRS Form 843
