"If the agent (a) is acting as an agent for two or more employers or is an employer and is acting as an agent for another employer, (b) pays social security wages to an individual on behalf of more than one employer, and (c) the total of the individual's social security wages from these employers is greater than the social security wage base, the agent furnishes and files separate Forms W-2 for the affected employee reflecting the wages paid by each employer." See IRS Rev Proc 2013-39.
Did your "agent" actually give you two W-2s? Did they put the agent's EIN on both W-2s or those of the original employers?
As I recall, at one point, the IRS started sending out audit letters to taxpayers who tried to claim the excess tax on the 1040; it was after this that TurboTax removed the agent screens that you spoke of.
Unfortunately, I don't see in the Rev Proc what one should do if the same EIN is used in multiple W-2s, it just says that it may happen.
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