WMG / The Enigma of Amigara Fault

The first victim of the holes was Slender Man.
The fact that he survived to become a Humanoid Abomination led them to revise the design a few times. The one at Amigara Fault may still be a beta.

The holes are a punishment on modern Japan for the mistreatment of the Ainu people
According to Owaki's dream, they were created as a punishment for terrible crimes by the people who inhabited Japan in prehistoric times. Perhaps one of their shamans had a prophetic vision, the way shamans do, that their descendants' land would be conquered by another race in the future and so they made holes shaped like the people in the vision as somekind of preemptive measure.