Zoom-in. Shinji is slumped down. There are lines from a nosebleed on his face.
MISATO (Off):“Shinji-kun!”
BGM END: E-6 [ANGEL ATTACK]
KnightmareX13: After nearly being boiled alive and being knocked unconscious, all Shinji has to show for it is a nose bleed?
FreakyFilmFan4ever: I'm not sure what it was about the Angel that caused Shinji's current nose-bleed. Especially since his earlier incident with Rei didn't result in any of that.
EvangelionFan: Looks like the obligatory nosebleed Shinji didn't get in Episode 05 Scene 05 has finally caught up with him.
Kendrix: Shinji's Synch ratio at this point wasn't high enough for him to sustain any physical injuries yet, but his psyche was still put though considerable strain - And perhaps reacted with a nosebleed. A nosebleed is something which involves ketchup (and as such allows the writers to show us that Shinji is badly hit this time), but it is also something that you can get for 'mental' reasons (One example for such a reaction being the sight of naked girls).
It is the most effective way the writers currently have to visually show us that Shinji's seriously injured here without using actual physical wounds yet.
(It is worth a mention that they DO give him a small first-degree burn (or at least a skin irritation, we see a red spot) in Rebuild.)
