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It’s possible that an employees net pay is more than the value you’ve entered when they are owed tax back, because they have paid too much up to that point.
Tax credits are divided through the year.  If you don’t get paid for one month in the middle of the year, that means you’ll get 2 times your tax credits for the next month’s pay.  This might mean that the employee is owed some tax back, and so their net pay is more than the value you enter.