Cant justify why money owing

I was at Sars last year and was told I owed money but upon speaking to the lady she said to me that if you have 2 IRP5s you will always owe Sars .How does a person whose salary is so low that he don't get taxed is suddenly owing money and all the lady can say is it happens that way.This is just a ******* to try get money out of a person because somebody needs to provide a detailed explanation for this