Marking the multiple jobs box on the W-4 for your lower-paying job instead of your higher paying-job can underestimate your total tax liability, resulting in too little tax withheld throughout the year- which could lead to:
1-Owing taxes when you file your return
2-Potential underpayment penalties and interest
3- Smaller paycheck adjustment now and larger tax bill later.
The form assumes the job where you checked the box is higher paying one and calculate the extra withholding accordingly. The IRS assumes you are earning more from that job than you actually are and your other job is less significant, so the higher paying job withholds at a lower rate and the lower job doesn't withhold enough either.
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