Do you mean that the polygrapher told you that you were having trouble with the drugs question?  If so, they're just trained/programmed to do that when they're going to fail you.  The reasons are quite simple.

Not many people are spies, as a matter of fact.  But lots of people have done drugs.  So, if they suspect you of using countermeasures  they'll guess that you were doing so because you're on drugs, and not because you're a spy, because there are probably several hundred times as many people who've used drugs who apply for that agency as there are spies who do so.

Incidentally, the National Academy of Sciences,  the most prestigious scientific body in the country--unless you ask polygraphers: they think it's horrible because they found copious problems with the polygraph--have calculated that if (1) the polygraph had a field accuracy rate of 90% (which it probably doesn't) and (2) it was calibrated to catch 80% of spies, then (3) Only 0.5% of the people who were to fail would actually be spies.

[I]t is reasonable to expect that each spy or terrorist that might be correctly identified as deceptive by a polygraph test of the accuracy actually achieved in the field would be accompanied by at least hundreds of nondeceptive examinees mislabeled as deceptive.

This and more can be found in the NAS report, on page 182.

Just remember that probably less than 0.5% of people fingered by the polygraph are actual security risks.  Millions of dollars were spent trying to find the one risk, hundreds of valuable careers were ruined--not only a terrible human cost but a serious one for the agencies that lose valuable personnel with great experience.  But, hey, the polygraph isn't subject to cost-benefits analyses like everything else is; it's special!

Like many of you, I was wrongly failed on the drugs portion of my polygraph exam with the FBI.  My question though is this:  Why is it that almost everyone with a story like ours cites the drugs question as the one that they were failed on?  I know there's a couple examples of other questions getting people, but it seems like at least 90% of the time, its drugs.

I wonder because many people, when hearing my story, have said, "Maybe they just SAY its drugs, but really, there's something else in your file they don't like."  Which, if true, would mean none of us have any idea why we're failed.

Given the recent news that the Justice Department has been trying to weed out applicants with Democratic leanings, is it not possible that we are being tossed for similarly superficial reasons?  Or maybe they're actually valid reasons (beyond our control, of course), but they don't want to tell us because future applicants would hide those factors?

I don't know if others have posted this question before, or if anyone in a position of authority has ever commented on the subject, but any answers you coulud give me would be greatly appreciated.  I am going to be filing an appeal soon, but I worry that making the case that I don't actually do drugs is irrelevant (though I will make the case anyway, as I do not want my record to reflect this lie).