If you check you are married and your wife works you would check box 2C and then in the additional jobs section put her income.

If you dont do that but you do fill in sectiom 3 that you have dependants witholding would be calculated assuming your income alone covered your entire family.

Or, alternatively, if both your wife AND you filled out section 3 that could cause an issue. Lets say you had 2 children and you filled out section 3 that is $4k less on your combined taxes. If your wife also filled it out that would be a second 4k off which would mean you were claiming 8k off your taxes. If your total taxes were 7k then you would have zero witholding.