I can only speak for myself. i found that there are many traits that define instinct; critical is survival instinct, then other modes lie passive in the consciousness (which everyone has, but ignore) the list has many twist and turns and depends on what the physical mind seeks. ex: "idiot savant" cognitive perception, the "mind/brain" is a very complicated organ that intrigues research in "behavioral function." (you pose n interesting question that is difficult to answer.)(subliminal vs literal)

Those times when you get the feeling you're being watched. Or when you enter a property and a cold and unsettling chill goes down your back. Or when you meet a new person and though seemingly normal something just doesnt quite sit right with you about them. Or a disturbing notion that danger is imminent or that a friend is in trouble despite any reason to believe so. — Benj96

I don't think an intuition that danger is imminent despite no sensory data to suggest this -- likely the human brain making correlations between uncorrelated events -- has much to do with 'intuition' that something about someone isn't quite right, which is the brain performing analysis on behaviour that the conscious mind doesn't understand.

I suppose the point of comparison is selection criteria. We have some understanding of why humans are inclined to draw correlations between uncorrelated events, and we have a lot of understanding of why humans need to make quick assessment, unhampered by slow consciousness, of a person's body language. Both are good survival traits, even if both are horrendously error-prone.

As which other cognitive functions, such as empathy, there's a difference between having the capacity to do something (nature) versus the particular learned implementations of that capacity (nurture). For example, you and I both assess the body language of a stranger unconsciously, but whereas my brain has learned to give weight to people whose eyes are too close together, yours has learned to give weight to people whose eyes dart around too much, with neither criteria necessarily consciously known of. (Examples ad rectum, don't read too much into them.)

Do what feels right. Eventually, after enough mistakes, you start to learn a little something every now and then. Usually. Only way some folks will ever learn anything, unfortunately. And who hasn't gone through hardship really?

Spider Sense! or as Aunt May called it, Spider Tingle or something along those lines. Ever notice that Spiderman's "instincts" are never wrong but it fails to keep him out of trouble? Peter Parker even dies at one time.

Also, the tone of the OP suggests that the instincts being considered are about impending danger. What about instincts that inform us of something pleasant and joyful? I haven't heard of instincts spoken of, written of in that sense.

Ergo, given Murphy's law (whatever can go wrong will go wrong), it would appear that our instincts in re looming dangers become vindicated more often than not, resulting in us believing our so-called instincts.