you might be looking for reasons but there are no reasons.

[Shinji is so close to falling asleep. He's warm and comfortable, which is something of a miracle, and it's even more miraculous with Nagisa touching his face and hair like this. At least half of the time, Shinji doesn't like to be touched; he doesn't like feeling too out of control. So it's really a pleasant change of pace to be drifting off with Nagisa curling into him, Nagisa's fingers intersecting with his hair...]

What?

[Nagisa tends to talk him to sleep, literally, rambling like an idiot, but Nagisa just said a bizarre thing after a lull in their one-sided conversation. It sounded like why didn't you tell me and about your wrists and Shinji's sleepiness is receding into heartburn. Shinji wears long-sleeved shirts to bed because that's what he always does. Sleeves so long that they engulf his wrists and then some. This is on purpose. It's to conceal the ugly marks on his skin from before.]

Go to sleep, Nagisa, [he says, his eyes still closed, his tongue strangely leaden in his mouth.]