Another possibility is that the background investigators talked with individuals that you never authorized to speak for you, who offered derogatory comments.
That's what happened to me.

This frustration applies to all aspects of the CIA's incompetent vetting process.

Of course in the case of the CIA, those f*cks will not give any specific reason for declining to offer employment.
The best one can do is to request their CIA file under the Privacy Act, and search for clues there, as I have done .
Of course, Agency polygraph results are exempt from disclosure even under the PA.

Does anyone know what the time frame is to get an official rejection when you have failed the poly?

Thanks George.  Fortunately I just started on a 5 yr contract and after that I will probably be ready to retire. I am still angry but trying not to think about it.  If I were younger I would be more upset. I wish I had never started this but at the time I needed a job.  When I went on the interview they told me about the process and said I could not start until this process was complete. I thought why not and 
I would get a temp contract in the in the meantime.  I would just as soon cancel the whole thing but it looks like I can't.  Since I agreed to take the job I have to let it run out. I don't even want the job anymore.  Maybe there is an Alien in my attic I don't know about.

I'm very sorry to read of your unfortunate and thank you for sharing it here. Sadly, it is an all-too-common story. The polygraph failure rate for people seeking direct CIA employment seems to be about 50%. Worse still, failing a CIA polygraph failure may have long-term adverse employment consequences for you, as it will make holding any security clearance with any federal agency more difficult. (See the message thread, Breaking News - If you are denied SCI, you are in deep SH*T!....)

I got a job offer from a company this past year doing CIA contract work. I cannot start until the TSC SCI/Fullscope is completed.I recently completed the 2nd polygraph.  I figured what the heck I have nothing to hide and I and my whole family was born the states so it should be a snap right? Wrong!  When I went for the 1st Poly the first set of questions were for National Security.  I thought: Wow easy.  I haven't come close to doing any of that stuff. The second was suitablity.  So many things flagged and I was so shocked.  Some were rephrased and they were fine.  Some others weren't and I had to come back.  I was so fed up that I didn't want to come back but I had already agreed to to do it with this company and I had no choice.  I thought what good would it do me to go back. I went back and same issues. This just doesn't seem fair to me at all!  I am the most honest person there is and it seems it doesn't pay to be a nice guy!  I don't do illegal drugs, I have never had foreign contacts nor do I know any, I never worked with classified material so I could not have passed on any secrets, I didn't lie on my FS86.  My life isn't that exciting and there is nothing to tell or hide.  If I did I would not have agreed to the stupid thing.  I told the people at the new company that I didn't think there was any reason to continue.  I have since gotten a job and i like it.  IT's good enough.  Not quite as good of pay or benefits but certainly okay enough.  The people at the new company just said "Dont' worry about it because everyone goes thru this".  But if you fail you fail so i am just going to let it ride out and not worry about it anymore.  After the second poly I would start crying everytime I thought about it.  My friends and family could not believe it.  They just tell me that: "you are a honest and wonderful person and you know that".  That doesn't make me feel any better. I am still angry.  Time heals wounds.  I don't care too much that I won't have this new job.  But I am angry that I am honest and haven't done a darn thing wrong. Yet I appear a lier and a bad person.