Last year I got such a notice from 'Roads and Maritime', stating I had an outstanding debt (not a chance*) and that I would not be able to conduct any business with them until it was cleared. Some time later, I received another letter to say that I was again able to conduct business with them.
No mention of what had happened but I ignored the first one - I had no need to do business with them and I couldn't be bothered dealing with it at the time. I suspect they realised their mistake but still have no idea what happened.
I suspect this kind of thing happens rather more frequently than any of them would care to admit.
* - I don't receive or claim any benefits and I haven't even had a Medicare reimbursement in years so it couldn't even have been another government department.