How? They busted huge criminal network and linked the app itself to a criminal gang. This is how the law enforcement should work. Every human right, including privacy, has limits and the purpose of the law and the due process to establish where those limits should be. It would be strange to expect that privacy of a human trafficker or drug dealer is protected more than the rights of the people they harm.
They intercepted and read the messages of most users, yet the number of arrests is significantly lower than the total number of SkyECC and EncroChat users.
Not only that, but they also have charged and are attempting to jail the creators of these phones/end-to-end messaging apps.
With what is happening it is becoming pretty much impossible to provide backdoor free communication tools within the EU.