His methods were flawed in that he thought he had pinned CommanderX as a leader of Anonymous, not that he couldn't figure out who these people were. He was trying to make Anonymous this centralized group when it isn't.

For a parallel example, look at Al Qaeda. People keep trying to make all of these Al Qaeda in X groups as one giant organization when in fact the only thing they have in common is the name and idea. 50 years ago there'd almost always have to be a personal connection for a group's idea to spread to another group. Now with the internet and other means of cheap and easy communication, it's easy for these ideas to spread anonymously. Anyone who identifies with these groups can take the ideas and run with them without the original group even knowing.

Law enforcement and governments are going to have a hard time figuring out how to deal with this, as their old tactics of decapitating the group's head doesn't work when there is no head.