Thompson did not appear that day so a warrant for her arrest was ordered by Judge Carrie Wainwright.
She was arrested on July 31 - the same day as the system was updated, Mr Ewen said.
Thompson spent 15 hours and 22 minutes in custody before reappearing before a judge who realised the error and released her.
"The warrant to arrest was unquestionably unlawful," he said.
Lawyer for the Crown Sean Kinsler said it what happened was "regrettable", but it was not the responsibility of the Attorney General.
"Ms Thompson ought not to have spent the night in the cells."
He said false imprisonment could not be applied in the case because no court staff member physically jailed Thompson or intended for her to be falsely imprisoned.
Also, no staff had arrested or detained Ms Thomson, meaning they were not guilty of arbitrary arrest and detention, Mr Kinsler said.
A former Wellington District Court staffer, James Keegan, said the court staff relied heavily on the CMS system.
But he said there was no nationwide standardised testing for staff to be trained on the system properly.
In the Wellington court, new employees had to watch more senior staff use the system and training was "ad hoc", because it could be months before they saw all the procedures performed.
Under cross examination, Mr Keegan said there were online training resources for staff who wanted to learn or refresh their knowledge of the system, but he said there was very little time in the day to access it.
Wellington District Court court services manager Anna Graham, who was not employed at the court at the time of the incident, said training was an "ongoing commitment" and staff completed training modules during their employment.
Under cross examination Ms Graham said if staff did not realise the dangers to people's liberty of failing to update the CMS system, managers should have known.
The system was updated with Ms Thompson's new court information eight working days after it should have been, which was too long, Ms Graham said.
"I would not view it as acceptable."
If staff had time during their day, they could undertake the online training to keep their skills up to date, she said.
Ms Graham agreed with Mr Ewen that new staff who were paired up with more senior staff would only learn everything needed if their partner trained them properly, she said.
The case continues tomorrow.