Protecting against self made webpage API

Sometimes I come over applications where the creators don't want people to be able to use anything else than their own interface. Often, there has been 3rd party software, but people ended up being banned for using it. This brought up a question in my head.

The server that hosts a website doesn't know anything other than the packets it recieves and sends. How would one go about protecting it against someone just connecting a GUI against all the buttons in some web page? Or maybe even just analyzing the packets and start to make their own identical ones? Wouldn't the traffic look just the same?