That's part of the problem with polygraphs...they can't winnow out partial or incomplete truths...for example, if the informant might be implicated or associated with an otherwise truthful answer, it may still display indicators of deception. For example, "Guandique" may have told him about the $25,000 for other reasons, with the Levy story merely as a peripheral issue: i.e., promising to split it with him for a favor, etc.
Of all the polygraphers I've met, they all say the instrument is not 100% accurate, but to a man, they all claim THEY are 100% accurate. Go figure.
And having taken those exams a time or two in my life, I am not impressed with the instrument at all.