I have received a form from Nebraska saying that they have disallowed my withholding because the W-2's submitted were for a different year - but I e-filed, so of course the printed W-2's were not submitted, only the electronic file from TurboTax. Now Nebraska wants their money plus a penalty. Does Turbotax have a problem with the file the submit to Nebraska?
The only thing the state revenue department would see is what was listed on your tax return for the W-2 input. They wouldn't see the actual form, so I don't know how they could claim anything about a wrong W-2 being submitted by you, as none was submitted.
The W-2 entry would come from a download from your employer or a manual entry by you. In either case, it is important to review the entry to insure that the information listed is correct. TurboTax would make their entry based on the information downloaded from your employer, not from an entry on your previous year tax return. It is possible that your employer made the wrong information available to TurboTax from the download.
I suggest you look at the return and see if the income entry and tax withheld is wrong, if so you will have to pay in the additional tax due. You can write them a letter and request abatement of the penalty if you feel it shouldn't apply to you.