There are a number of reasons why this could occur:-
1) If a new employee - you may not have entered previous pay and tax data. A new employee normally provides a P45 which details previous pay and tax figures. Check to see that you have entered these figures into the system.
2) If a new employee - the tax was calculated incorrectly by their previous employer. The package uses figures entered from the P45 to calculate the current tax due. If the employee previously paid too much tax, because it was calculated incorrectly, the program adjusts the tax in the current pay period accordingly and this may even result in a tax refund.
3) If a new employee - he/she may have been unemployed for a period of time Since tax is normally a cumulative calculation, the tax free pay allowance for pay periods in which the employee did not receive a payment are carried forward. Check the date on the P45. Has there been a break in earnings?
4) If an existing employee - a pay period may have been missed out/skipped/not updated. If your employee is on a cumulative tax code, a skipped pay period may result in a tax refund, the next time their pay is processed.
5) If an existing employee - has there been a change to your employee's tax code. If so, the employee's tax free pay allowance may have increased leading to a tax refund being due this week/month.