Looking into his eyes, she knew he spoke the truth.
"She's lying," I said with certainty.
He clearly believed what he was saying.
Righty-ho. Maybe our hero saw the suspect leaving the scene, so he knows for a fact that she's lying when she says she was never there. Perhaps our hero is the suspect's lifelong bestest best friend, and feels able based on that to judge whether she's telling the truth. Possibly our hero is actually psychic. In these cases, the reader is usually made aware of the relevant facts.
Or, ooh! Maybe the author wants to stop that line of questioning and proceed in another direction, so we need to believe this loose end is tied up, which doesn't work if the person in question might be lying. Or perhaps our heroine is about to rough the suspect up, and would seem like a jerk for doing that if she wasn't sure he was lying.
This is especially common with characters who are trained as psychologists, or are cops, or grew up on the streets and had to learn to read people, or are just "very intuitive." There are any number of qualifications that render a character able to act as a lie detector. Only, you know, reliable. Unlike actual lie detectors.
I personally can't claim any degree of this ability. It sometimes takes me a moment to realize people are even being sarcastic. If someone were actually trying to deceive me, I fear the chances of my recognizing that fact would be perilously slim.
But I'm not alone! I recently read the excellent - if eerie - article "On the Psychology of Confessions: Does Innocence Put Innocents at Risk?" by Saul Kassin. This paper, which spans many experiments and case studies, explores the question of how good people actually are at telling whether or not other people are lying. Not good, as it turns out. Furthermore, training - such as that given to police interrogators - did not statistically increase their accuracy, but did increase their confidence in their accuracy. (How's that for scary?)
While the whole article is a fascinating read, the fact that grabbed me most comes from a footnote. "After testing more than 13,000 people from all walks of life, O'Sullivan and Ekman (2004) have thus far identified only 15 'wizards' of lie detection who can consistently achieve at least an 80% level of accuracy in their judgments" (Kassin 2005). (I would cite the original work, The Wizards of Deception Detection by O'Sullivan and Ekman, rather than citing a citation, but the original is a book rather than an article I can just read online and link to.)
That's about 0.001% of people who are consistently correct in distinguishing between truth and lies . . . at least four times out of five.
So even the 0.001% of humans who are the absolute best at telling truth from lies might still be wrong as much as 20% of the time.
I'm sure there are rogue super-wizards who are correct so consistently that they are, for all practical purposes, accurate lie detectors. Still, it would be nice for writers to keep in mind that this is extremely, extremely rare. Just being a cop or psychologist or a streetwise con artist does not qualify a person to sniff out falsehoods.
Naturally, this doesn't preempt a character's believing that s/he is super-accurate, or that someone else is. But if a character actually is reliably accurate, the writer should perhaps be aware that that character has been endowed with an incredibly rare ability. (Or possibly absurdly good luck.)
Besides all of this hard-facts stuff, I typically find characters more relatable when they're unsure about who to believe in these situations. It also gives a scene more depth and tension when the character and the reader aren't sure what's true and who to trust.