Hi,
I applied EA for Princeton. My common app was submitted at like 11pm pacific time on November 1st (but past midnight in Jersey), so I think I am okay on that part. My application materials from school did not make it to Princeton until a few days ago (transcripts, rec letter, etc). There were a few miscommunications with the school on where to send the transcript and my teachers were very behind on submitting rec letters-actually one of them hasn’t submitted hers yet, and I asked her back in September. What should I do? The parts of the application that came in late were mainly out of my control, since the school was in charge of sending transcripts and rec letters… should I email princeton with an apology? Would this negatively affect my application? I did get an interview offer, though. Is this whole late application dilemma going to ruin my chances at Princeton??
They will not hold your teachers actions against you. However at a certain point without the right number of recs they will have no choice but to judge based on what they have. So the teacher needs to send it in
first of all, breathe! The application time stamp uses your local time, so you’ll be fine. For the recommendation letters and other parts where you have no control over, they will not hold you to it. The rec letters and transcripts can be late. Plus, they don’t start reading the applications until about two or three weeks after the deadline. You’re good!! 
You aren’t good if that teacher delays much longer. Go see them in person tomorrow, and remind them when the app was due and that decisions are coming out in less than a month. Politely ask if they will be able to get it in this week.
A bit of advice for future applications: don’t wait until the last day and stay on top of your recommenders–a friendly e-mail reminder a week before the deadline would be fine. You don’t want to give a school ANY excuse to reject you. And bad things happen when you wait until the last second–what if you got sick, your computer died, or your internet crashed? With that said, best of luck.