The article states that there was a period where Pokémon Go was removed from App Stores temporarily, but the servers remained up, and that people illegally downloaded the game in order to play.
In other words, as long as you get the app from official app stores, you have a legit version.
For example, compare it to roms. You can buy Pokémon FireRed authentic from the store, or you can download it online from a sketchy website. It’s the exact same thing, except with PoGo.
It’s not a particular “version”, but rather a time period where people used pirating methods of getting the game, and some people attached malware onto the file since they knew it would be downloaded.
Just like anything, anywhere; downloads can contain malware if not installed from a trusted source.
Hope this helps! Let me know if you need any other clarification
