Is there any example of automatas (or similar) systems that emerge complex internal structures on its own?
It seems very hard to define the phrase "internal structures that defend their own existences" in a rigorous or precise way, so it is not clear that the question is well-defined.  However, some very simple systems can admit behavior that might be described in these terms.

For instance, consider Conway's game of life.  It is known to allow for replicators: i.e., there are self-replicating patterns which create a complete copy of themselves.  Replication can be thought of as a "strategy" for "defending your own existence"; if you spawn many copies of yourself, then even if someone messes up one of the copies, the other copies will still exist.

So, to the extent that the phrase "internal structures that defend their own existence" is well-defined, self-replicators in Conway's game of life might be considered a form of internal structure that will defend its own existence.

Conway's game of life is very simple.  Another very simple example is Rule 110, which is an extremely simple cellular automaton.  It is known that Rule 110 is Turing complete, which means that it is possible to simulate Conway's game of life in a Rule 110 cellular automaton, which means that a Rule 110 cellular automaton can be argued to allow for "internal structures that defend their own existence".  It's probably going to be hard to find a system that's much simpler than a Rule 110 cellular automaton.



In general, we should probably be careful about anthromorphicizing the behavior of computational systems like this.  Just because they behave in ways that resemble the behavior of people or animals doesn't necessarily mean it's necessarily going to be super-meaningful to describe them as acting with a 'purpose' (like self-defense).  Ascribing human motivations or emotions to them runs the risk of misleading our intuition.