Misato:“"I'm the one who's in charge of your operations, right?"”
Shinji:“"Yes."”
Misato:“"You have a duty to obey my orders. Understood?"”
Misato:“"Don't do it again."”
OMF: Misato's comments here are only confirming what Shinji already feels. She's his commander, and he's her subordinate. Nothing more.