He saw what nobody else seemed to.
When Kakashi-sensei stepped through that door and the eraser fell on his head, he found it hilarious and he couldn't believe that this guy was a Jonin. They were the best, after all. And yet he couldn't spot a simple trap like that?
But... then he had a chance to study his new sensei while they were on the roof.
The way he held himself, ready for anything and everything to happen in the next instant, and ready to react to it.
The way he looked. His clothes were clean, sure. He obviously hadn't had a mission in a while, or he recently did laundry. But, he could see the small tears and patch jobs that littered his uniform. A small stain, here and there. They looked brown, but he wasn't  that naive about the ways of the shinobi. Small burns here and there on his flak-vest, a rip near his shoulder that he clearly felt didn't in any way compromise the vest itself or he would've replaced it once he noticed the damage. He knew Iruka-sensei had needed a new vest after everything with Mizuki.
His headband, though... if he thought Iruka's headband was old and worn, that was nothing on this guys headband. The ends were frayed and there were burnt spots on the edges of the fabric, and more brown spots. The metal plate had recently been polished, but there were dents and small scratches all over it, though none covered up the Konoha symbol in the middle. There was one spot on it, where it looked like the plate itself had been twisted and bent out of shape, and then bent back into shape.
The way he smelled. Like earlier stated, he was clean. But the old smell of blood still clung to him and to his clothes. Underneath the scent of old blood was the smell of lightning and electricity, and fire. Clearly he used a lot of lightning jutsu.
He knew now.
This wasn't a mistake. This guy didn't miss that trap. He let the eraser fall on him. He wanted them to underestimate him.
There was no doubt in Naruto's mind that this wasn't just a Jonin in front of them.
This was a Shinobi.