I think if the government said “these workers are no longer legal and we are revoking their visas” like they did to TPS immigrants that would make more sense.

To make up evidence en masse seems a whole other level

It's a horrible situation. No evidence was ever produced against the woman in the article. She was just verbally accused by interrogators; which unfortunately is a tactic that is often used by law enforcement. They are permitted to lie to suspects in the course of an investigation. Having found no credible way to charge her with any crimes, they revoked her work visa (which apparently they can legally do without any cause or justification needed) and she was deported.

It seems that everyone on that ship was having their work visas revoked regardless, and on the way out, the authorities were trying to find out how many they could charge with a crime as well.