Bonuses (i.e. supplemental income) are subject to higher withholdings (not to be confused with tax rates). The simplest method that most small businesses use to withhold on bonuses is the flat 25% method.
Source?
My hunch is that it's a problem with the payroll system being used, or how the bonus is being entered, which might be annualizing the income.
I know of someone who qualified for SSI for a disabled child. However, the mother worked for a school that was often behind on the payroll. Every time the school played catchup, and gave a check (or multiple checks) that were supposed to be paid over an extended period of time, but were now all paid in one month (or one quarter) the SSA annualized the income, resulting in the SSI being withheld, demand for repayment etc. etc. The family didn't understand why this kept on happening, it was just a regular bothersome ritual for them to keep on going to the SSA. Until they came to me for help on another issue, and when I looked at this scenario, I realized what was going on, and suggested that they ask the school to make a special exception (it's ridiculous that this should be the case) and pay this teacher on the same schedule as the goyishe workers (who would never tolerate delayed payments), so that they don't face this hardship.