From beneath the part of her face gouged out by the Angel, an eyeball appears.
Reichu: Both here and in EoE, the Evangelion eye socket is given a "stylized vulva" look that I find hard to ignore. It makes a little sense if you consider that a new eyeball is "being born"… I don't think the resemblance is entirely in my head, either. When I showed the series to a friend of mine, at this point she abruptly commented, "It's a vagina!"
Mr. Tines: I wonder whether this may be a case of "sometimes a cigar is just a cigar", as, after all, there are only a few possible choices for the geometry (pore, mouth, possibly the few-pointed star like Sachiel's palm may be). The mainly horizontal alignment of the feature, and the symmetry about a line perpendicular to the length of the slot are what one would expect of an eye. This contrasts with the key geometric cues of the vulva, which are a vertical alignment and an asymmetry about the perpendicular axis.
Reichu: Sure, they're not "anatomically accurate" if they're meant to be "faux-vulvae" of sorts — but, then, how often is anatomic accuracy a requirement for the inverse concept, the omnipresent phallus? Even if you put the eye socket stuff aside, there are at least three instances in EoE that really, really stretch the whole "cigar is just a cigar" bit; IMO, Anno is definitely using "subliminal female genitalia" to mess with our minds.
FYI, this "bubbling" of flesh is a recurring motif in NGE, tending to accompany either metamorphosis or regeneration (which are similar concepts, in a sense).
Also, if EVA-01 really has relinquished control of her body back to her keepers, why is she regenerating now? This is the sort of thing she can obviously do of her own accord, but while Shinji is in control?? Not to mention it's rather odd that this is happening now, as opposed to during the battle (when Sho bothered to stop and heal her arm).
HeWhoPostsStuff: Methinks the answer's obvious: She wants to freak him out. After a hard day's battle one has to unwind a little, after all.