Agree with scaevola about our brains looking for patterns. It is a very primitive instinct about protection - hearing a distant twig crack, the feeling that someone is looking at you, the sense that someone is a little too close, the instant recognition that someone as been in your cave room and moved something by a minute amount..... And all of these visual, smell, hearing (etc) sense are in the very primitive part of our brain - located quite far from the higher thinking part.
So the rational, logical, emotionally happy brain is telling us everything is OK, and the primitive brain is shouting "Watch out!"
However, because we also have a higher functioning brain that is clever and reasoning and deductive (and also protective), we sometimes see patterns where there are none: we can see every man as a cheater (and interpret innocent behaviour as such), we can imagine that every burst of anger is a prelude to a violent assault...
And ultimately the real life skill is being able to learn the difference, and learn when it matters.
If I was walking along a street alone and the hairs on my neck stood up - I'd trust my instinct. Something (whether dangerous or not) had made me alert and I'd take the cautious route. If I had a 'funny unexplained feeling' about my dh, then I seek out other sources of information gathering and validation.... I might be right that 'something' is happening, but I could be wrong about what it is.