Dumb Question about Federal Withholding Rates

So, I have taken over doing payroll and am new to this and am trying to streamline it.

So - previously we would give one check for pay, one check for an auto allowance on the 4th week of the month.

I combined the pay and auto allowance onto one check (becsaue, why not?) and now there is ~$30 more in Fed WH being taken out than was on separate checks. wth?

I have looked up rates, but Everything seems to be auto in Sage. We can clearly see it's only the withholding that's affected, but there is no way a $225 Auto allowance puts everyone in a new tax bracket.

?