After the earthquake at the beginning, Lucius said that Poseidon was unhappy. Poseidon is a Greek god. Lucius should have mentioned Neptune, the Roman counterpart of Poseidon.
Throughout the movie, Romans and Hebrews alike casually talk about Yahweh. On their way to Galilee, the Apostles even begin the Lord's prayer with "Yahweh, hallowed is your name." No Jew, Apostles included, would dare pronounce the name of God, except the High Priest in the Holy of Holies of the Temple in Jerusalem, and he would only do it once a year for Yom Kippur. Jewish people would use other terms, like "Adonai" (Lord), "Haqadosh" (The Holy One), and "Hashem" (The Name).
In the movie, Pilate and Clavius are concerned about an upcoming visit from the Emperor. Historically, Emperor Tiberius, who was in power at the time, lived on island of Capri, near Italy. He refused to leave it for very long, even to return to his rightful dwelling in Rome. He never paid any visits to any province of his empire so distant as Pontius Pilate's district in Judea.
Under duress from the Sanhedrin, Pilate finally orders Clavius to have just two of his soldiers guard Jesus' tomb. Whether one of Pilate's auxiliary units, the Sanhedrin's temple guard, or some combination was assigned to guard the tomb, known historical Roman and Judean practices dictated that the entire detail had at least 15 troops, allowing them to set up several shifts so they could take turns guarding the tomb four or five at a time while their comrades slept.
Mary Magdalene is portrayed as a prostitute. She is arrested for questioning as she enters a tavern known to be a place for soliciting potential customers. Her identification as the woman caught in adultery, and as a prostitute in general, are based on medieval legends which have no canonical or historical foundation. The New Testament indicates that she was one of Jesus' followers because he had exorcised a number of evil spirits from her.
The label on top of Jesus' cross says "Jesus the Nazarene, king of the Jews" in Hebrew, Greek and Latin, as mentioned in the Gospel of John. While the Hebrew text looks correct, the Greek and Latin lines appear to be horizontally mirrored. However, reversed script was common in the first century. Plus, the relic known as the "Titulus Crucis" (its authenticity is in doubt, but it alleges to be the inscription on Jesus' cross) is actually written in reversed script, so the movie is likely deliberately copying the artifact.
The movie shows Jesus' arms pierced just above the wrists. Those who have received the "stigmata," such as St. Francis of Assisi, show wounds at the palms. Common Roman practice at the time was to nail the condemned at the wrists, with the arms supported by ropes. The movie's depiction is likely correct.
Clavius and other Roman soldiers on horseback have saddles with stirrups. Stirrups were not invented for at least 50 years afterward.
A scene features a modern marine hourglass in 33 CE; the device did not exist prior to the Dark Ages.
During the cremation of Roman soldiers outside the fortress walls, Clavius salutes a dead friend and says, "legion ten". The tenth Roman legion, the Legio X Fretensis, were not garrisoned in Judea until 73AD, 40 years after the depicted crucifixion.
As the Roman approaches Jesus to lower him from the cross, a radial airplane engine can be heard.
Early in the film, Clavius is depicted alongside many Roman soldiers doing battle with zealots just outside Jerusalem, led by a man named Barabbas. Assuming this Barabbas is likely the same zealot mentioned in the New Testament freed by Pontius Pilate in place of the condemned Yeshua, there is no realistic way for him to have been in both places (being freed from the Fortress Antonia and doing battle with Romans in the desert) at the same time, as this could have only happened a few hours prior to the start of the film.
When they meet in the desert, a bearded dragon lizard is perched prominently on a rock. Bearded dragon lizards live solely in Australia.
Agaves and Opuntias are from the Madrean Region, and could not have appeared in the Holy Land until the discovery of Americas.