Now, I'm not sure about chickens, but from working with a cat/dog vet for a long time, I can tell you that tapeworms are one parasite that often do not show up on a fecal exam. It has something to do with the fact that their larval/adult stage is different. So it's probably not the vet's fault, it just wasn't the right time for the tapeworm to rear it's gross ugly head.
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