Why does my wife owe in the state of VA if her state of residence is CA? She’s active duty military and stationed in VA.

Yes, your wife should not need to file a Virginia state return if she didn't have any other VA income (side job, etc). Only her State of Legal Residence has the right to tax her military income but California won't tax her military income while stationed outside California.

Please make sure she selected only California as her State of Residence:

1. Login to your TurboTax Account 
2. Click "My Info" from the left side of your screen
3. Click “Edit” next to your name
4. Please scroll down to “State of residence” 
5. Select "California"
6. Select "No" to "I lived in another state in 2022."

If your wife didn't have any other Virginia income then she can delete her VA state return.

Please see What is my military state of residence? and Civilian pay earned by active duty military for additional information.

I believe she put the information in as you explained but it’s saying she owes in VA taxes.

In the My Info section, be sure she checked "Yes" to the statement "Served in the U.S. Armed Forces in 2022".

Remember that only her military pay is exempt from Virginia taxation.