Ela está admoestando ele. Esta presumivelmente não é a primeira vez que ela o pega ficando acordado até tarde para ler sua papelada quando deveria estar dormindo.
MARGARET: Two in the morning. I know I didn't wake you? [Why the hell are you still awake?]
WHITMORE (filtered): As a matter of fact you did. [I certainly wasn't up reading my paperwork, honest!]
MARGARET (smiles): Liar. [You clearly were awake, you naughty President/husband!]