My wife works for a company based in VA and who have deducted VA tax from her Paycheck. It's a very negligible amount since that happened only for one of her Paycheck at the end of December.
We live in MD and I have aleady filed jointly my Federal as well as MD returns. As per VA Taxation I do not need to file a return but my question is how do I get the VA tax amount that was deducted from 1 paycheck.

Also her company keeps on deducting VA taxes even though we do not stay in VA (she works in VA and we stay in MD). They say that since they have many employees all over the country working for clients they always deduct VA taxes.

If your wife works in VA (physically present in VA), this is VA source income of a nonresident. She must file VA tax return and pay VA taxes.
Then she will report same income on the MD tax return. On the MD tax return, she will claim credit for taxes paid in VA.