No, the polygraphs are VERY VERY accurate.
They measure what they're supposed to do and do it well.
The problem is that the people ADMINISTERING the polygraphs are, after all, only human.
Plus, there is no standard ruling body for polygraph education and administration, so while you have some very good PIs that spent time with police work, detective work, and completed intensive polygraph education courses and are certified by the national organization, you have others who took a fly-by-night class that do the same thing but with much less accurate results.
That being said, you can have the same test shown to two different testers - one with 30+ years experience and one with 2 years.. chances are the 30+ veteran will have an accuracy rating of well above 95%.
That is not, however, acceptable as far as courts go. They can't have uncertainty when distributing justice, and that is why polygraphs are not admissable.