I was against the idea of contacting POIs after submitting the application but as time passes by and I hear nothing, I am tempted to do so. What do you think? In fact it could have been better to send a short email right after submitting but now it is very late and all. But maybe he will say you are rejected/accepted etc. so that I will know in advance.
Just write that there has been some problems and that you want to fix it. It can turn out OK. I applied when the deadline has passed but they still allowed me in. They are pretty flexible when these things happen. Nothing wrong with writing and asking at least.
Upenn did interviews last week last year so maybe we will hear something this week at least interviews etc. Cornell sent some acceptances around this time too last year so I am very hopeful. January seemed so long this year.