If they do find something that they think is questionable but still want you in, they will most likely do a secerity interview with the applicant after they have finished thier investigations. They will bring it up at that point and grill you about it. Even then you may still get the clearance depending on what the nature and sercumstance of the incident. The one thing that I think we will all argee on is "DON'T LIE ABOUT ANYTHING", on the application or in an interview. If you lie and they find out, you won't be left with enough clearance to go to the bathroom by yourself.