What the title and bot don't mention: They did so by installing spyware on phones of users of a vpn they acquired:
After Zuckerberg’s email, the Onavo team took on the project and a month later proposed a solution: so-called kits that can be installed on iOS and Android that intercept traffic for specific subdomains, “allowing us to read what would otherwise be encrypted traffic so we can measure in-app usage,” read an email from July 2016. “This is a ‘man-in-the-middle’ approach.”
What's more:
Later, according to the court documents, Facebook expanded the program to Amazon and YouTube.
Obligatory this is why you shouldn't use a free/cheap vpn.