In this movie, characters are prominently seen handling apples and pomegranates. Pomegranates were considered the "original" apples, and were symbols of strength to the Persian armies.
The "Hassansins" were modeled on the infamous Persian mystery cult called the Hashshashin, from which the word "assassin" is derived, given their use of terror and assassinations as political leverage. Their leader was named Hassan Ibn Sabbah, whose activities took place in the heart of the Alborz Mountains of northern Iran (the place was called Alamut). Legends have surrounded the indoctrination process of the members of the Hashshashin cult, which are said to involve drugging and mind control. They were likely inserted as an homage to Ubisoft's largest franchise, "Assassin's Creed," which is likewise based on the cult of Hashshashins.
Mentions of God or "the Creator" are references to Zoroastrianism, the religion practiced by Persians until Islam became popular. Zoroastrianism does not have a concrete concept of Hell, despite Nizam mentioning it. Tamina worships an unnamed set of gods, which are briefly presented in juxtaposition to Dastan's beliefs.
During the invasion of Alamut at the beginning of the movie, there is a scene where Dastan is about to jump off of a wooden contraption. He stops for a moment to get his bearings, during which the camera focuses on him while moving around him in a circular motion. While this very unique scene never happens in any of the Prince of Persia games, it is an iconic feature of the Assassin's Creed franchise. In all of the Assassin's Creed games, the assassins ascend to high vantage points to get their bearings, an event that is presented in a nearly identical fashion and with similar musical cues as the way it is presented in this movie. This is likely an intentional homage to Assassin's Creed (which was created many years before this movie), as the "Creed" series is considered to be the spiritual (and more successful) successor to the Prince of Persia series.