I feel like listening to your gut is a big component of this. There have been times when I notice that the way someone talks bothers me for a reason I can't put my finger on and I decide to give them the benefit of the doubt, assuming I'm being shallow or unreasonable, but then a few months or even years later their behavior lines up with my initial discomfort and I realize I had spotted something being off from the start. Sometimes it's better to listen to the general feeling you're getting from the less verbal and analytical parts of yourself than to wait until you have a real explanation.
Of course, there may be people who are just anxious or a little eccentric and that's what you're spotting, but usually it's worth at least sniffing it out from a distance rather than fully ignoring those feelings until you can articulate the reason for them.