If the W-2 shows taxes paid, then technically you should be off the hook. This is something the IRS should be taking up with your employer.
It sounds like they may not have processed your W-2.the IRS mailed me another notice that they disallowed my claim for refund because they "couldn't verify the total federal withholding amount" I reported on my tax return.
For your return, they should be going by the W-2 attached. The W-2 has the employer info, and if they haven't received taxes, then they should be going after them. It looks like the state processed your return like it should be.