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Well, my experience has been to ALWAYS trust my animals instincts. Dogs, cats and horses, in particular. If my dog bristles up at someone, I'm going to use extreme caution, if not outright hostility, in my interactions with that person. If my lady's cat backs up and bristles at someone, same applies. A horses reaction can be harder to read, but if you know what you're looking at, it may as well be a flashing sign, in plain English.
Animals are consummate judges of character. They do have a "sixth sense" but, its the nose that knows. My Elkhound once cued on this guy, an acquaintance of my then GF. This dog was as friendly as it gets. He had never shown aggression toward anyone. But, this guy, now...his hackles stood and a growl that I didn't know he was capable of put me on Red Alert. He , immediately, moved between me and this guy, and was locked on like a HARM missile. He was told to leave, and NEVER come back.
My coydog was far less ...subtle..in such cases. He would attack, and was a lethal weapon. I would always leash him when strangers were around. If he sensed bad intent, his solution was far less diplomatic than my Elkhound. Yep, the nose knows. Trust your companion.