The force had put out a statement saying “anyone who declines to be scanned will not necessarily be viewed as suspicious”. However, witnesses said several people were stopped after covering their faces or pulling up hoods.
Campaign group Big Brother Watch said one man had seen placards warning members of the public that automatic facial recognition cameras were filming them from a parked police van.
“He simply pulled up the top of his jumper over the bottom of his face, put his head down and walked past,” said director Silkie Carlo.
“There was nothing suspicious about him at all … you have the right to avoid [the cameras], you have the right to cover your face. I think he was exercising his rights.”
Ms Carlo, who was monitoring Thursday’s trial in Romford, London, told The Independent she saw a plainclothed police officer follow the man before a group of officers “pulled him over to one side”.
She said they demanded to see the man’s identification, which he gave them, and became “accusatory and aggressive”.
“The guy told them to p*** off and then they gave him the £90 public order fine for swearing,” Ms Carlo added. “He was really angry.”
A spokesperson said officers were instructed to “use their judgment” on whether to stop people who avoid cameras.
"Officers stopped a man who was seen acting suspiciously in Romford town centre during the deployment of the live facial recognition technology," a statement said.
"After being stopped the man became aggressive and made threats towards officers. He was issued with a penalty notice for disorder as a result."
Eight people were arrested during the eight-hour trial, although only three were a direct result of facial recognition technology.
A 15-year-old boy identified by the cameras was arrested on suspicion of robbery but released with no further action.
A 28-year-old man was arrested on suspicion of false imprisonment and another man, 35-year-old man, was arrested on suspicion of breach of a molestation order.
The other arrests were two teenage boys accused of robbery, a 17-year-old boy accused of firing a gun and two men, aged 25 and 46, for drug possession.
The deployment trial was due to continue on Friday, but rescheduled because of forecast snow and cold temperatures causing "low footfall".
Monitors saw several other people stopped outside Romford station, in north east London, including a student who had pulled his hood up and a man handcuffed and put in a police van.
Activists from the Liberty human rights group said they spoke to a youth worker who was stopped because he “looked like someone” on a watchlist, but had been misidentified.
Scotland Yard said the two-day deployment of cameras in Romford would be the last of 10 trials of the controversial technology.
The Independent revealed that more than £200,000 was spent on six deployments that resulted in no arrests between August 2016 and July last year. Two people wanted for violent offences were arrested after a trial in December.
Critics have called the force’s use of facial recognition a “shambles” and accused Scotland Yard of wasting public money.
Automatic facial recognition software compares live footage of people’s faces to photos from a watchlist of selected images from a police database.
Any potential matches are flashed up as an alert to officers, who then compare the faces and decide whether to stop someone.
The Metropolitan Police has described the deployments as “overt” and said members of the public were informed facial recognition was being used by posters and leaflets.
But no one questioned by The Independent after they passed through a scanning zone in central London in December had seen police publicity material, and campaigners claim the technology is being rolled out “by stealth”.
Detective Chief Superintendent Ivan Balhatchet, Scotland Yard’s lead for facial recognition, said a full independent evaluation will be carried out.
“The technology used in Romford forms part of the Met's ongoing efforts to reduce crime in the area, with a specific focus on tackling violence," he added.
“As with all previous deployments the technology was used overtly. We continue to engage with many different stakeholders, some who actively challenge our use of this technology."