Without having direct contact with the employer, it is hard to tell why they did that, however, the IRS does not control the W4 or how much extra you have withheld.
When you file your W4, if you want you could have an extra $1,000/ pay withheld (assuming your check is high enough).
You can try submitting the W4 again and watch her checks each week to be sure the correct amount is being withheld. The School district should be using the 2022 Tax Withholdings to calculate the amount she has withheld as a starting point. Any changes you want to be made would be done through the W4.
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