This is a question that is often asked by nervous students getting ready to submit. Applicants imagine a dark nebulous hole that engulfs their application and consumes their hopes of getting in. Often they think that an application is passed over, forgotten or lost in some drawer. In reality every application that is received by student services is vetted by several individuals. It is the general practice that any application which does not meet the requirements be checked by at least two people.
Once an application has been vetted one of a few things occurs depending on the program. In general the applicant receives an email stating that their application has been received and is in process. Any missing requirements are noted in the initial email that goes out. Students are encouraged to ask questions at this stage. If there has been an error their application is rechecked and corrected right away. The best way for an applicant to resolve an issue would be to respond to the email they received.