What would you do if you found out you had serious security problems after the fact? That's the whole point of it. You have these going through at a secret level. It's not like we are talking routine; it has “secret” stamped all over it.
This is mind-boggling. These contractors came in and did the whole job. You say there were some mitigating circumstances, but it wasn't a full security clearance. What if, when you did a full security clearance after the fact, you ran into a situation like the NORAD one? We'll come back to that in a minute, but where would you be then, and who would be responsible?