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.
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...
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.