In the film, the Serapeum is on top of a hill. According to certain authors, it contained only part of the Great Library's works after its fire 500 years earlier. There were two libraries, and the Great Library was on the other side of the Rhakotis quarter, in front of the Island of Pharus.
Bird's-eye and satellite images are used to contrast the story's earthly developments and the universe Hypatia tried to disclose. These images show 400 AD Alexandria along with modern man-made Suez Canal, Assuan Dam, Lake Nasser, and Toshka Lakes..
In one scene, the Capitoline Wolf is in the background, with the figurines of Romulus and Remus. The twins were added in the late 1400s. Debate exist over whether the statue is from the 5th century BC or the 13th century AD.
At the end of the movie, Johannes Kepler is correctly credited as the actual discoverer of the elliptical nature of planetary orbits. However, his discovery hinged on the very precise measurements of his contemporary, Tycho Brahe. The deviation from circularity is far too subtle to have been measured by any instruments available to Hypatia more than 1000 years earlier.
The film refers to Hypatia as an atheist. She was a Neoplatonist, adhering to a philosophy of contemplation towards perfection. This idealistic monism sought truths from any worthy source, including pagan and Christian worship.
Although the film shows Synesius abandoning Hypatia and attacking her theories when she refuses to convert to Christianity, in reality it was Hypatia who broke off all contact with Synesius. No record exists of his ever having tried to convert her and his letters to her even after she refused to respond are full of glowing praise for her, begging for a reply. His last surviving letter was written to her.
A major plot line is the Christians' destruction of the Great Library Library. According to historical accounts, Alexandria's vast stores of scrolls and knowledge were destroyed almost 500 years before the events of the movie. Contemporary accounts of the Decree of Theodosius attribute the loss to the Cesarean destruction in 48 BCE.
In the film, Bishop Synesius condemns Hypatia's works and refuses to support her before severing all ties. In reality, he defended her scientific reputation and maintained his correspondence with her, which remains the only contemporary account of her life and influence. No record exists of him ever trying to convert her .She refused to reply to any of his letters praising her for reasons she never disclosed to him.