For tax withholding purposes - the bonus is treated as supplemental wages.
There are two ways to determine federal tax withholding from supplemental wages:
- flat 25% withholding, or
- to add supplemental wages to regular wages for that pay period and withhold from the combined amount.
Most companies use flat 25% withholding because it is simple and clear.
So we might guess that is what your company is using.
In case the person overpaid taxes with withholdings - the overpaid amount would be claimed as a refund on the tax return.
Let me know if you need any help.