Projection. Sometimes someone's mannerisms or the way they look unconsciously remind us of someone from our past that we had negative feelings for. Hence that first feeling of hate, or even feeling uncomfortable by being around them for no specific reason.
Bad experience with them in a past life? Subtle indicators from the person your subconscious picks up on that the person may be unsavory to you in some way? prejudgemental tendencies based off of past experiences with people who looked or acted similiar? Some people just exude nasty in their aura or bioelectrical field? Not part of the human race entirely and you can sense the difference between them and you or they you and them?