Rei goes “!!”,
super close-up of her opening her eyes wide.
REI:“!”
Kendrix: Rei is has just realized that Shinji was crying because of HER all the time, and she is completely shocked at the fact that a complete stranger would show such a strong emotional reaction for her sake, more so than your average girl since she thinks her life is valueless.
When Gendo saved her, she grew very attached to him as a result, but he is her creator - Shinji has, from Rei's viewpoint, absolutely no reason to worry about her. She has just formed a new bond, a kind of bond that she didn't know before - hence the shocked reaction.
NemZ: Yep, you can see here the exact moment at which Shinji stops being just an annoyance and instead becomes someone she actually cares about.
