Bonuses generally count as part of annual salary. This means your friend will get less money than he's expecting in that paycheck, because the tax rate for that paycheck is calculated as if he was getting that much every paycheck. (So, instead of calculating it based an increase of $1000/year, taxes will be deducted as if he'd gotten a $24,000, or $26,000, or $52,000/year raise.) That in turn means he's likely to get a refund when he files his taxes for this year, but if he was thinking "what will I do with the extra thousand dollars," he may be unpleasantly surprised when it's only half that.
In other words, it looks like a different tax rate for this check, but when he looks at the numbers for the full year, it's the same tax rate.