There is someone in my office who makes my skin crawl, and I know he has the same effect on some of my colleagues (male and female) too. Nobody has a single example of anything inappropriate or weird that he's ever done, but lots of us for some reason find him creepy. The poor bloke is almost certainly perfectly harmless but for some reason I can't shake the notion that he must be a massive wrong'un. DP (who works at the same place as me) once said 'I'm convinced that one day I'll see that man on the front page of the papers for his part in setting up a weird new age cult where all the members are convinced the apocalypse is happening next Tuesday'.
The 'gut instinct' thing, where we subconsciously pick up on small cues without realising it that tell us someone is dangerous, is all very well. Sometimes it's absolutely correct. But it has a massive flaw, which is that we also all have unconscious biases and subconscious recollections that we're not even aware of, and these often make us nervous of people for completely the wrong reasons.
For example, people are unconsciously biased in relation to things like race, neurodiversity, age, appearance, religion and all manner of other things - we think we aren't, but we are. And those unconscious biases mean the 'cues' we're picking up without realising it are often completely skewed.
Similarly, we all have associations in our heads that we're not even aware of. Often when we find someone a bit creepy and 'just can't put our finger on what it was, but just had a bad feeling about them' it's actually because they're wearing the same kind of shoes as someone we were scared off as a toddler or something. For every time someone is massively creeped out by someone who turns out to be a murderer, there are 1,000 times that someone is massively creeped out by someone who is perfectly harmless.