How do we even know those holes are 500m years old? You cannot carbon date a rock (that's when the rock formed, not when the hole was made). Perhaps we're missing evidence of earlier civilizations in plain sight
It’s well worth reading about this. The ways that scientist have determined these things are complex but easily discoverable on the Internet.
Also, while I was using hundreds of millions because that was the timeframe of the original question, the reality is that we actually have fossils that are more than 3 billion years old.
