It would appear that Clark, as he grows, is coming into his powers. Presumably this is perfectly normal and happens in a way that's analagous to puberty. On that particular day, he suddenly became able to use both his super-vision (x-ray, infra-red/ultra-violet) and his super-hearing. There's no mention in the novel of a particular trigger, only that it was somewhat new and totally overwhelming.
The other children giggled at his discomfort. They couldn’t see what he saw—the inside of Ms. Whitaker. The teacher’s skin and clothes had gone transparent, revealing the bones, organs, and arteries beneath. He could see the blood coursing through her veins, watch her heart beat rhythmically. Her lungs expanded and contracted like fleshy balloons. Chewed-up food made its way through her digestive tract. She looked like the “visible man” model he’d seen in the Sears catalog, but life-sized and pulsing with animation. Exposed muscles, resembling strips of raw meat, covered her bones. Eyeballs rolled in the sockets of her skull.
He looked away from her, only to discover that his classmates had turned into living anatomy lessons as well. Even worse, he could hear all of their heartbeats, which were pounding like kettledrums—and growing louder by the second.
Clark threw his hands over his ears, but it didn’t do any good. He could hear everything. Even the ticking of the wall clock sounded like a jackhammer going off right in his ears.
It was unbearable.
Man of Steel: A Novel
Notably, Zod and his followers go through the same learning curve when they land, albeit much much quicker and with far greater self-control. This strongly suggests that these traits are related to physical maturity rather than the total amount of time spent in Earth's atmosphere.