You can mail the MIT Admissions about this. You should always avoid situations like these. Can you get another [4th recommender] to quickly send a recommendation to solve this problem. The 3rd recommender then can still send the letter after submission. 

I'll never understand why so many applicants wait to the last minute for this sort of thing. You knew the deadlines months in advance. Is this how you're going to approach your grad school assignments?

@natematt I know what you mean, and I know I invited your comment with mine, but I don't actually think applications and assignments are very analogous to each other. A graduate school application is a very basic and straightforward checklist of requirements, with the occasional vague detail that needs clarification. But it absolutely has to be complete.

A project, on the other hand, can pursue countless different directions with countless different influences to be considered/implemented/rejected, yielding a product that is the result of countless design decisions by the student. And that product is understood to be unfinished; it is simply the best work the student could produce in the allotted time.

More relevant, arguably, is that any single assignment is of limited individual importance, while a graduate school application that is incompletely submitted or shoddily assembled can cost an applicant admission to the school of their choice, potential financial aid, or another year's wait to reapply. Grad school decisions make huge differences in a student's life.

My point was unclear, but what I meant was that a grad school application is so much easier than graduate school assignments. If this person was to post in a year about how his/her grad school critics are 'so harsh' and 'unfair,' is anyone going to have any sympathy when just getting a basic application in on time was too much to ask?