<p>Since the deadline is strict, and MIT has a very scientific way of working, missing the deadline for so long without explaining or waiting for the EC’s information to show up though the deadline has passed might be judged to be an unscientific behavior. However, because your counselor told you to wait, I think you should explain the situation (stress your counselor’s role, but don’t speak like blaming him/her). They might tolerate the mistake which wasn’t made by you. Though they might have bad opinion about you, I think it won’t be as bad as doing nothing to set up the interview. Anyway I’m just an applicant, so don’t rely much on my advice.</p>