How did Virginia come into the picture? If your wife worked in Virginia, even for just a few days, she has to pay Virginia tax on the money that she earned for working in Virginia. The employer is correct to withhold Virginia tax for those days, and your wife has to file a Virginia nonresident tax return in addition to her California resident tax return.

Her employer is located in VA but she does not work there at all. 

She should ask her employer for an explanation of the VA withholding. As others have explained , that's not right.

As to the 2% of the time, she works outside CA, see: http://money.cnn.com/2013/06/28/pf/taxes/business-traveler-tax-threat/

If your wife neither lives in nor physically works in VA, she should submit VA Form VA-4 to her employer, checking Box 3.  Here's a link to the form:

https://www.tax.virginia.gov/sites/default/files/taxforms/withholding/any/va-4-any.pdf