Repayment of sign-on bonus in the same tax year it was received - tax withholding amounts reduced

I received a sign-on bonus of $10,000 this year that I repaid this year (2024). I'm not sure why, but they only asked me to repay around $6,000 of it.

 

They received my sign-on bonus. I checked my paystub today, and there are negative amounts for this period's pay for the following items:

 

Federal Withholding Tax

Federal EE Social Security

Federal EE Medicare Tax

State Withholding Tax

 

Since I only returned a portion of the $10,000 to them, I assumed the portion I didn't return was paid to the IRS. Is this the normal thing to happen for sign-on-bonus repayments for the same tax year?