How much is taken out of your paycheck is determined by Form W-4, which is a withholding statement. What likely happened is that when your wife filled out the form with her job, she filled out the form as married, and then perhaps said she had several dependents (Note: on the W4, the dependents are called allowances). The higher the number she put, the less tax would have been taken from her check, especially if she makes considerably less money than you.
She can change this by refilling the Form W4 with her employer, and selecting the status of "Married, but Withhold at the Higher Single Rate". Also, she can reduce the number of allowances she claims as well, and the end result should be more tax withheld, and, more refund to you.
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