Liability orders are dealt with by Magistrates Courts as it is a criminal offence not to pay Council Tax

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The court will only be concerned with proving/disproving the liability for the non payment of Council Tax, and there are very few grounds for non liability. The Court will probably take the view that although a direct debit was set up on your bank account and the council didn't claim it as per the payment schedule, you are still jointly and severally liable for the full amount and issue the liability order and if it did get into the courtroom you will be asked as to why you did not notice this mistake originally and query it earlier.
You have several options available to you:
Pay the full amount on the summons, including costs, the day before the hearing. This will remove any liability.
Go to Court on the hearing day and make an arrangement to pay. The liability order will still be granted.
Go to your Council offices and speak to a manager in person, try to negotiate a mutually agreeable settlement.
In any case, whichever course of action you decide to take, make a formal written complaint to the Council following their own complaint procedures. This will enable you, if you are not happy with the outcome, to take it to the lcal Government Ombudsman.