Similar experience, part of my application was misplaced and my application was not forwarded before the end of January. In the end my file was only "complete enough" with parts missing that were in the same envelope as the parts that they did receive. The admissions office does not make it a secret that they rather not have you pestering them checking your materials, but then again, unlike some other schools, they will not alert you if there is something "missing" from your file either.
I guess these things can and do happen, the question is whether our cases are incidents or GSAS has more structural problems. Either way, it does bug me a little, seeing that Columbia was one of my top choices. I would hope that my application had at least gotten full consideration.