Kyle: ... All animals should run free.
Scully: Even if that means trampling a man to death?
Kyle: Maybe he should have gotten out of the way.
Mulder: I'm sure he would have if he had seen it coming.

Willa goes out to hunt the tiger in the office building with only a tranquilizer gun. It is higly doubtful a zookeeper would go after a tiger with only a tranquilizer, as it takes a few minutes for the tranquilizer to take effect.

Wouldn't the zoo animals have to been abducted twice? Once to the aliens to artifically inseminate the animals, and again to "harvest" the embryo...