When Jesus visits Jerusalem as a young boy, his family walks past the outer wall and travels past the crucifixion site where Jesus would be killed later in the movie. In this early scene, the crosses and scaffolding have already been set up with the same Roman guards who appear later in the film (set 30 years in the future) already posted by the crucifixion hill. Consider however, that crucifixions were a regular occurrence of the time, so this locale would have been established and regularly used. Anyone portrayed early and later in the film should have been shown to age appropriately given the passing decades.
When Mary cradles Jesus' dead body, there are no lash marks on his back.
The movie scripting refers to Pontius Pilate as a "procurator", a specific post that differs from the one that the Gospels imply that he held - prefect or governor. Historically, Pontius Pilate's title was thought to have been procurator but an inscription on a limestone block - apparently a dedication to Tiberius Caesar Augustus - that was discovered in 1961 in the ruins of an amphitheater called Caesarea Maritima refers to Pilate as "prefect of Judeaea". Archaeologists believe it to be genuine. In this instance, the Gospel account is supported by archaeology, since the surviving inscription discovered at Caeserae states that Pilate was prefect and the movie should have followed also as it is based on Gospel accounts.
In real life it was Roman Soldiers who nailed Jesus to the cross. In the film, Jews working for the Romans nail Jesus to cross.
Just after Jesus is baptized by John, in one scene it shows him walking up the hill with the lower 1/4 of his clothes still wet from him bowing down in the water. The camera shifts to view John watching Jesus walking away and then comes back to Jesus, but this time his clothes are completely dry!
When the children torment Mary Magdalene (Anne Bancroft), one boy blows up a plastic balloon and throws it into the fire, causing it to pop. Plastic was not invented until the early 1900's.
The celebration of becoming a Bar Mitzvah, which Jesus is shown participating in, was not developed until medieval times.
Many of the Roman Soldiers have beards which isn't correct. Roman Soldiers and Romans in general at the time always remained clean shaven.
Full-immersion baptism, not sprinkling baptism, was in use at the time of Christ.
Pilate asks Jesus if he is a king. Jesus responds, "I am," but his lips say something else. It appears to be the start of his previous line beginning "If my...", although the shot looks slightly different. Perhaps it was an alternative take of that line.
When Jesus' body is taken down off the cross and laid on the floor, one of his eyes blinks slightly.