You do have to pay back. While it's a payroll error, the fact is that they undercharged you. It unfortunately underlines the importance of ensuring that you check your payslip and make sure you understand fully all of the deductions and the basis on which they are made.
The fortnightly deduction will probably - indeed, should - have been expressed to you in two ways: firstly, that it is a percentage deduction which is linked to salary, and secondly what that actual amount was at the time. If they did not inform you that it was a percentage deduction they should have done, but I do not believe you would have any recourse against them since the terms and conditions are set out in a number of circulars.
As the arrears may now be moderately substantial, it would be reasonable for your employer to offer you the option of going immediately to the correct deduction level and making an agreed payment plan for the arrears if you are not willing / able to pay them at present.