In every case that I have had negative gut feelings about people, those feelings have born themselves out to be true. Some of the time I ignored them, thinking that it was just my own closed-mindedness or a kind of prejudice. However, I now believe that it is actually based on a set of cues that we take in, but don't necessarily consciously process. For example, someone who has an irregular way of making eye contact (too much, not enough, lots of blinking, staring, etc) makes us feel uncomfortable. There is nothing that they've done so far that would make us believe them to be a bad person, therefore the thought often isn't consciously noted. However, it does register that it's different than the usual pattern of good interactions. If we were to think about it, we'd realize that a person that does that could be merely socially awkward or insecure (which should govern how much we trust them or how we interact with them), or it could be an indicator of mental illness, strange thoughts, attempts to manipulate etc (which also should put us on our guard).