Despite their use, polygraphs and the biological indicators that they measure is known to be inaccurate which is why many states and countries do not allow them in court.
lawinfo.com identifies the problems this way:
"The accuracy of lie detector test results can vary depending on the person administering the test, the machine used, and the person taking the test. As such, polygraph results are generally not admissible in criminal cases."
Apa.org goes further into the psychological factors and the unproven causal nature in these tests:
"The accuracy (i.e., validity) of polygraph testing has long been controversial. An underlying problem is theoretical: There is no evidence that any pattern of physiological reactions is unique to deception. An honest person may be nervous when answering truthfully and a dishonest person may be non-anxious.
A particular problem is that polygraph research has not separated placebo-like effects (the subject's belief in the efficacy of the procedure) from the actual relationship between deception and their physiological responses.
One reason that polygraph tests may appear to be accurate is that subjects who believe that the test works and that they can be detected may confess or will be very anxious when questioned. If this view is correct, the lie detector might be better called a fear detector.
The cumulative research evidence suggests that [Control Question Tests] detect deception better than chance, but with significant error rates, both of misclassifying innocent subjects (false positives) and failing to detect guilty individuals (false negatives)."
These tests can also be beaten deliberately:
"Evidence indicates that strategies used to "beat" polygraph examinations, so-called countermeasures, may be effective. Countermeasures include simple physical movements, psychological interventions (e.g., manipulating subjects' beliefs about the test), and the use of pharmacological agents that alter arousal patterns."
There are also plenty of online resources training people to beat lie detector tests.
Other factors known to affect a polygraph test are depression and anxiety as well as medications used to treat them.
An social psychologist and professor who specialised in polygraph tests for over 30 years, Leonard Saxe, says “Polygraph tests are not a valid technique for assessing truthfulness [despite sometimes being] required for jobs requiring a security clearance. [...] Assessing autonomic nervous system reactions to questions about one’s history should not be part of how individuals are selected for sensitive jobs.”