The Serapeum was on the top of a hill. According to certain authors it contained only a part of the works of the Great Library after its fire occurred centuries before. There were then two libraries and the Great Library was in fact on the other side of the Rhakotis quarter, more or less in front of the Island of Pharus.
Bird's-eye/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 (created in 1998).
In one of the scenes the Capitoline Wolf is seen in the background with the figurines of Romulus and Remus. However, the twins were added only in the late 15th century AD, so only the wolf statue had existed at that time. (Moreover, it is questioned nowadays whether the wolf statue itself is indeed from 5th century BC, or was manufactured in the 13th century AD.)
Although Johannes Kepler is correctly credited at the end of the movie as the actual discoverer of the elliptical nature of planetary orbits, his deduction was only made possible by employing the very precise measurements made by his contemporary, Tycho Brahe. The deviation from circularity is far too subtle to have been measured by any instruments available to Hypatia - more than a millennium earlier.
In one of the movie scenes a quite large Opuntia (Prickly pear cactus) can be seen. These plants are not native to the old world and they were introduced to Africa after discovery of the Americas. In fact, Opuntia was introduced to Europe at the beginning of the 16th century by Spanish seamen.
There is one cactus"shrub" that is shown several times, also the the juicy fruits are eaten by the locals. This makes one wonder, have the Spanish movie-makers deliberately done the cactus a "part of the plot" ?
Although the film explicitly refers to Hypatia as an atheist on a number of occasions, 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.
Although a major plot line of the movie is the destruction of the Great Library by the Christians, the actual Library of Alexandria and its vast stores of scrolls and knowledge were (by historical accounts) destroyed almost 500 years before the events of the movie. Contemporary accounts of the Decree of Theodosius make no mention of this massive collection being destroyed, attributing this loss to the 48 BC Cesarean destruction.
The film depicts Bishop Synesius condemning Hypatia's works and refusing to support her before severing all connection with her. In reality, like many contemporary Christian scholars, he defended her scientific reputation and maintained correspondence with her that remains the only contemporary account of her life and influence, and far from Synesius abandoning her, she refused to reply to any of his letters praising her for reasons she never disclosed to him.