The only way to know his reasoning is to ask the employer. However, it could be due to some entries she made on her W-4. One such reference encourages this:
How should married couples complete W4?
Your spouse should claim all the allowances that the Two-Earners/Multiple Jobs Worksheet says you, as a couple, are entitled to claim, and then you would claim zero allowances on each Form W-4 that you complete for your two jobs. W-4
Another possibility is that someone who works part-time had a lower weekly/biweekly salary. Employers go by a chart the IRS publishes that tells them how much to take out based on the income and the exemptions on a W-4. If the income is low, the withholding is low.
