He’s unhappy that his father is absorbed in that object, not even noticing that he’s there.
MAN (OFF):“It’s decomposing rapidly so using it as material would be highly problematic.”
Ikari (behind):“I don’t care. Throw the rest away.”
Man (OFF):“Yes, Sir.”
Shinji turns away with an expression that suggests he’s thinking “I guess someone like me doesn’t even matter…” but then he looks at Ikari again in puzzlement.
Eric Blair: Besides the obvious "I need to be a 50 feet diameter red sphere for you to pay attention to me?" part, I like how Shinji's face when noticing Gendo's hands still show the emotion of saying "My dad got injured... how?"