He registers asphalt, rough despite the visual of a flawless smoothness, traces of dirt that seem to skate along the surface, but when he presses down, it's sickeningly springy, flesh-soft, humid like cooked meat.— Map of the World, ch 8
The holes are presumed to have been created by Lucifer in response to Dean Winchester's arrival thwarting his victory during the Apocalypse. As the only thing that can dissolve creation is Creation itself and God is currently absent in the narrative, Lucifer is the only one still left on earth with the power to turn creation to its own destruction and unmake reality. The night Endverse Dean was killed and Dean Winchester arrived, the prophecy that Lucifer had been promised of how the world would end ceased to follow, and he responded by using his Grace to tear thousands of holes in reality.
He's not trying to destroy the world."
"Then what the hell do you call this?"
"If I were to make a comparison," [Castiel] answers, "I would wonder if the kitchen was covered in broken dishes because someone had a terrible day.— A conversation between Dean and Cas, Map of the World, Ch. 8
The holes are not just superficial. Lucifer used his Grace to reverse the process of creation and unmake reality. Left in their place is absence, not just of what once was, but of anything there had ever been or will ever be.
Creation itself was dissolved [...] There's nothing here, Dean: it's absence. Not just of everything, but of all that was and is and will be, and on every plane of existence. There is nothing here, not even reality itself.— Castiel of Chitaqua, Map of the World, ch. 8
The result is a wound in reality itself, a void where nothing exists that compels anyone who is close enough and looking into it to continue to do so into perpetuity. The holes themselves don't do anything, but while the human mind can't comprehend the dissolution of reality and can't form memories enough to grasp what it is looking at when there is nothing there to grasp, it would nonetheless keep trying with single-minded focus until the body gave out, which makes them dangerous.
- Map of the World ch. 8
- Map of the World, Ch. 8
- It's the Stars That Lie, ch. 5