You're making a lot of assumptions. You're assuming that it's that easy to make a self-replicating probe that's that intelligent, for one. Any civilization that advanced may have put a lot of thought into what such probes should do, and how they should interact with other civilizations. They may very well have come up with the Prime Directive and only observed, without becoming detected by primitive cultures such as ours.

You're assuming that there aren't other spacefaring civilizations out there who are opposed to these probes, and that don't actively seek them out and destroy them.

You're assuming that the galaxy and nearby vicinity is old enough for one of these civilizations to become this advanced and to build these probes and for one of them to reach us. Who knows, maybe there just aren't that many really old civilizations around yet. Just look at how long it took us to evolve to this point.