It's all-too-common for truthful persons to wrongly fail the polygraph. In fact, the procedure is inherently biased against the truthful, because the more honestly one answers the so-called "control" questions, and as a result feels less anxiety when answering them, the more likely one is to wrongly fail.

For a detailed explanation of polygraph procedure and suggestions on how to reduce the risk of a second false positive outcome, see Chapters 3 & 4 of The Lie Behind the Lie Detector (1 mb PDF):

https://antipolygraph.org/lie-behind-the-lie-detector.pdf