Box 15 of my W-2 has two different employee IDs, both in the same state. Box 16 reflects that each has different amounts. TurboTax tells me "The state in box 15 should only appear once" and won't let me move forward to file. Is the W-2 prepared incorrectly? The W-2 reflects two separate locations I do work for, both in the same state.
If it won't let you move forward in the program, I would just combine the two in a single TurboTax entry. It won't cause you any problems.
@DavidD66 is correct. Combine the two amounts. This is a change in the way some businesses are now structured, and TurboTax has not made the necessary updates. Use the same EIN that they used for federal and keep the W-2 with your tax records in case some computer has a question about it.