At first I wondered why Scully, when trailing the young man from WAO, climbs over the fence instead of going to the entrance. Then, when Mulder drives up, he finds the entrance locked, and climbs over the fence, too! Why didn't Scully notify anybody at the zoo that she was trailing a suspect and to have some guards at the ready, and be given a spare set of keys?

Even with the music on, I can hear the clicking of Scullys shoes on the paved road inside the zoo when she is running after the young man, but for some reason, the young man doesn't hear that somebody is following him.

Phil already mentioned the tiger-outside-the-cage incident, where the invisible tiger mauls the young man, but I wonder: why is he directly outside the cage at all? Previously, I thought the bright light was the transporter beam. But directly after that, the invisible tiger is outside the cage - wouldn't the aliens need some time to implant/remove an embryo? Besides, the visible tiger returns in the city, not in the zoo. So, did the transporter alien make a mistake and instead of beaming the tiger up merely make him invisible and transport him a few meters? (The transporter guy was having a bad week anyway, with his "astrological" variance etc. )

In the teaser, the invisible elephant makes the ground tremble, a window crash, and demolishes quite a few cars etc. Could one elephant really cause this much? I could understand a whole herd of elephants making the ground tremble, but one?

Strange that Kyle Lang from WAO doesn't seem to know (or doesn't mention it onscreen) that animals who are raised in captivity often aren't able to live in the wild, because they never learned how to cope. At least Sophie would have been shipped to a wildlife reservat. A big step forward if she was found in tarif barracks only 10 years earlier. But why then ship her cruelly in a metal box, without a human to calm her?

Why is Willa accused of Kyle Langs murder, if Ed Meecham killed him without her orders, and she wasn't present to prevent it?

Why did Willa not fire Ed Meecham years ago? If the WAO has proof that he still mistreats the animals, and she knows he previously mistreated them? Is the town so short of helpers that he is indispensable? No member of an animal org. would be willing to help instead?

I wonder: when Sophie signs "Human help Human", was trying to get Mulder to help her, thinking of herself as Human rather than ape? (Other language-taught apes think of themselves as humans, I've heard).