Step 1) Go to the My Info page and DELETE WV as an other state that you work in. For tax purposes, you only work (effectively) in VA since only VA taxes were properly withheld, and since VA and WV have a reciprocal tax agreement that allows that.
Step 2) Go the State section and delete the WV tax return all together. You don't file in WV at all. (Only exception would be for people form VA who own rental properties in WV, or who work in WV as self-employed individuals)
That should clean it up. Try to remember that for next year.
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It works the other way for WV residents working just across in VA .
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*