- Americans Hate Tingle: The film did not find much success outside of Spain.
- Anvilicious: Belief Makes You Stupid and Axe Crazy. While this is not to say that some people throughout history have committed atrocities and then rationalized such actions with their religious beliefs (e.g. the Great Anti-Buddhist Persecution, various Jihads, the Crusades) and should be called out when they do happen, but this particular historical event as portrayed in this movie was not as clear cut as it was in real life.
- Ho Yay: Occasionally averted because Christian males were much closer than nowadays (for instance, kissing another man's hand was a sign of respect, not homosexuality), but there's some genuinely suspicious examples here and there. For the record, the director is homosexual...
- Narm Charm: "An Ellipse!"
- Tear Jerker: The destruction of Alexandria's library, the death of Hypatia, among many other moments.
- Values Dissonance: For all her rationalist outlooks, and although she tries to be nice to her slaves, Hypatia is perfectly fine with the institution of slavery. This is a plot point; Davus is obviously quite intelligent and shares Hypatia's interest in science, but his knowledge that he never will be recognized as "equal" in a traditional, pagan society drives him into the arms of a radical Christian sect, the Parabolani, where he is regarded as equal despite his status.