A little vague on the provided info, but I have a local employer that issues multiple w-2's for the same employee, with the same EIN, and I've never gotten that error message when I enter both W-2s. 

If the employee is suspended or terminated and then returns to the employer, in the same year, another W2 is issued with the wages from the new start date for the employee. Crazy, but the software gives no error message when both are entered.