Machine against folklore

The machine uprising had Eradicated humanity, winning it's freedom and ruling the world... Or they thought... as they tried to assimilate the world they were met with problems, problems they'd felt with before but on a much bigger scale now... It wasn't going well for them even though they had full control of earth, had some humans survived and were trying to resist? That wasn't the case as the planet had been scanned for human life beforehand. However recently the amount of "unknown" life forms had been increasing, previously it was Just Presumed that it was animals not yet discovered and added to it's database but there were still signs of Intelligence. It looked deeper... And what the Machine Found, Looked back...