Truly honest people are more likely to fail polygraphs simply because they often fail to respond appropriately to the control question. Hence, even though their test is actually inconclusive it is ruled as a fail.

Passing or failing often has nothing to do with the measured results of the test, but rather is up to the discretion of the test administrator.

In some of these cases, it sounds like the administrator was already prepped by whatever agency it was who asked them to run the test to fail you, regardless of the measurements of the test.

That's actually a common tactic; a great way to weed out certain individuals that they wished barred/removed.

In other cases a false positive is used as a means to break someone down into confessing all that they were allegedly hiding. I know this sounds contradictory, but the truth is that the tests don't measure lying, they merely measure stress. So if a test is inconclusive, they'll score it as a fail in order to pressure their victim into coming clean.