This is the conversation in episode 3:
ミカサ : 違う。
ミカサ : これで私と離れずにすんだと思って安心してる。
Literally, it translates to
Armin: (His; Eren's) eyes are telling "How's that!".
Mikasa: (You're) wrong.
Mikasa: With this, (He; Eren's) relieved thinking that (he) doesn't have to be separated from me.
The word in (parentheses) is the omitted subject.
Mikasa's words is a response to the conversation in dining scene (which was slightly omitted in the anime)
From post no. 382 on 2chan,
When Mikasa told Eren, "You shouldn't aim to be a soldier anymore",
Eren, who couldn't dispute it, was staring at Mikasa annoyed while thinking "I understand even if you didn't say it!".
Mikasa misunderstood Eren's expression as "Looking from his staring, he hates to be separated from me".