It's not just Centrelink. I had $3090 taken from my tax refund. I phoned the ATO and they said I had a tax debt. Some years ago my only income was an Australian Postgraduate Award which was not taxable. So I thought I didn't have to lodge returns for that period. My bad - but the ATO didn't tell me there was a fine or fee for not lodging. When I was back in paid work and lodged a return the system asked me to lodge the missed ones. I did. There was no indication that I had a penalty to pay. I received tax refunds for several years and then this year they deducted the "tax debt" from my refund, with no notification or explanation. But the ATO people are pleasant and helpful; the one I spoke to sorted it out, cancelled the debt and refunded the full amount.
It seems absurd that I had never been billed for this "debt". But the ATO acknowledged that shortcoming, and were easy to deal with.