There would be thousands of perfectly circular holes drilled straight through many older layers of rock, with casings, from fossil fuel extraction. They would presumably be filled with sediment, but still obviously artificial.
We have fossils from the Cambrian period ~500 million years ago that include many traces of holes from burrowing animals. We've identified animals from ~500 million leaving many different kinds of traces as well as from fossils. 500 million years from now humans will have left many remaining traces. While older fossils are rare and precious, there's no generalized entropy that just destroys all old things (until there's a supernova/mega-meteor/etc., eventually the planet will be gone with enough time). In the right conditions much can be preserved for hundreds of millions of years. Many human artifacts like gold and other inert metal tools will be around besides the many physical changes we've made across the surface of the Earth.
There is one constantly happening thing that wipes the slate clean - tectonic plates movement. You can be lucky with a spot that doesn't disappear into Earth's mantle, there are few spots like that on Earth, but its not granted.
While it is true that over deep time less and less survives due to subduction not all areas do, and human activity covers vast surfaces now leaving many artifacts and traces. You should also consider that we do have fossils from > 3 billion years ago. Certainly not everything will survive but there’s no question some human traces will persist for hundreds of millions of years.
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.
There's more. At the same time oil well holes are drilled many orders of magnitude deeper making them cross thousands of strata rather than being limited to a meter or two. Most oil drilling is in areas prone to subduction but there are areas in Canada where they're drilling over surface rocks that are hundreds of millions of years old. Those won't subduct soon and are far more discoverable than an animal burrow due to size. We've got around 1 million active oil wells in N. America, fewer than animal burrows, but in areas they'll be preserved in deep time and in sufficient numbers there's a reasonable chance of discovery.
