Penalties deducted from pay out?

I looked on the SARS eFiling and it stated that I should pay them a big amount of money (I assumed it was for late tax returns). A week later they paid out a small amount, after a consultant said we do not owe anything on their system. Am I correct in assuming that they deducted the penalties from the tax returns and paid out what was left? Or should I still be worried about that letter?

They usually deduct the penalties and if SARS says that nothing is owing anymore then that should be ok.