These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Inferred Holocaust: At the end of the film, people who have lived 400 years within Bregna decide to leave the city for the untamed jungle. And even with fertility reoccurring, there is no guarantee that everyone of child-bearing age is fertile. (In fact, it was only about 20 women in the whole city who had become pregnant in Goodchild's sample group.)
In Name Only: Pretty much the only things the film has in common with the animation are that the two main characters are an assassin named Aeon Flux and a scientist/dictator named Trevor Goodchild, and that cloning occurs.