Our brains register tons of information when people communicate with us, it goes way beyond just the words that are spoken.
Point is that the so called "gut instinct" is actually your *brain* warning you that there is a disconnect between the verbal language and the body language cues. Your brain recognizes lies, half truths or exaggerations that the "heart" may not be willing to acknowledge. That funny feeling in your gut is a direct response to your brain's message that there is a threat to safety present. It's actually an evolutionary relic that helped our ancestors survive.
Trust your brain, not your heart.