We are residents of CA. My wife's company is in MD but took out taxes for VA (we used to live there). I don't know how to handle this.

[JulieCo]

It depends. 

If you were living in VA during 2018 when the VA taxes were taken out, you would need to file a part-year resident return for VA and allocate income to VA for the time period you lived there.  

If you did not live in VA during 2018, then you will need to file a non-resident return for VA and record that the income earned in the state was $0 in order to get refunded the VA taxes. 

Below is information on filing part-year (first link) and non-resident (second link) returns, for you to choose which one you need depending upon your scenario as noted above:

https://ttlc.intuit.com/replies/3302008

https://ttlc.intuit.com/replies/3302052