The facial recognition is likely 'only' used as a pursuit/detection mechanism. Presumably/hopefully when making a case in court they use traditional evidence like eyewitness identification, DNA, etc.
Novel evidence like this is probably unlikely to do well in court for the reasons you describe.
In the specific instance described in the article, the police and prosecutor failed to produce any more evidence than the facial recognition match.
Nevertheless, they imprisoned a man for ten days, and proceeded to press for criminal charges over the course of the year. As described the man had to spend his entire savings on this defense.
The court system worked correctly, in that the judge told the prosecutor to produce more evidence. The charges were dismissed.
So we have the "happy" ending of a man whose life has been turned upside down, whose financial situation has been ruined, and who has had to spend his time and effort defending himself rather than contributing to society in a positive way. All because facial recognition was used as the only piece of evidence.
Novel evidence like this is probably unlikely to do well in court for the reasons you describe.