What I mostly find information on is the idea that bees can smell fear and will attack someone afraid of them. Though bees and wasps likely can sense that a person is around by the various chemicals we give off, they probably cannot sense fear, and anyway they would not attack a person just because he was frightened: there’s no reason to. More likely, bees become interested when they “smell” a foreign animal around and investigate; the person becomes afraid and tries to swat the bees; the bees feel threatened and sting.
I know that doesn’t really answer your question about flies…is there a source you know of saying that they do smell emotions?
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