How did aliens on a habitable planet hide themselves during the recon and scouting stage by human colonists?
We've found a habitable planet orbiting a red dwarf star some light years away and conditions are Earth-like enough that a colonization project was initiated. Before any humans landed on the planet, a thorough, extensive reconnaissance of the planet was done.
After we reached close to the planet, we parked the colony ship in orbit to get housekeeping done. We surveyed the surface from orbit, we did tests on the weather, we sent out probes nearby and studied the star carefully. Probes and drones were also sent through the atmosphere to figure out its makeup, and then to the surface. We brought back samples of microorganisms and the local flora back to study and see if everything is kosher from a safety standpoint.
The only caveat is that we did find ruins of some kind of advanced civilization on the planet, but no signs of the actual inhabitants themselves. The study of the planet is not cursory - we've been examining it for years with our colonists waiting in cryosleep. No stone is going to be left unturned.
But here's the thing - there actually are intelligent aliens on this planet, and for their own nefarious purposes, they've been hiding from humans until they're ready to show themselves.
So my question is - how did they manage this disappearing act, with us combing the planet with a fine-tooth comb for signs of life. To make it easier, let's say that the population for the aliens is fairly low for a Earth-sized planet. Let's say there are about 50,000 of them on the planet.
What could they do in order to stay hidden? Underground habitats perhaps? Maybe we didn't think to look too deep below the soil and they managed to stay unnoticed?
What are some other ways they could hide?
I have to give partial credit to gianluca, whose answer inspired this, but... what if They live in the ocean If your a …