(at around 1h 20 mins) As Robert is running towards the fence in the cemetery of Cervette, you can see his raincoat already has the tear and blood stains from his impalement on the fence, though he has not yet reached the fence.
Gregory Peck's hair color changes throughout the film. In most scenes it's grayish, but especially towards the end of the film (presumably these scenes were shot after the film was completed) his hair is completely dark.
(at around 19 mins) When the priest is physically escorted out of the building and down the steps by two guards, pedestrians can also be seen close-by. When the photographer takes a picture of the priest walking past him on the steps, and develops it, neither the security guards nor any pedestrians can be seen anywhere in the photo.
(at around 1h 4 mins) When the taxi driver in Rome first exits the cab, his finger is bandaged. A minute later, it has no bandage.
(at around 37 mins) When the photographer takes a picture of the priest the second time, in the park, the picture is taken at a distance of many yards against a background of trees and tall shrubbery. The developed photograph shows the priest in close-up with no vegetation at all.
The poem recited by Father Brennan to Thorn, and later read out of the Bible by Jennings and quoted to be from the Book of Revelation is in fact NOT found in the Bible and was written specifically for the film.
(at around 38 mins) The process for revealing a photo goes like this: Revealer, Water, Fixer and Water. When Jennings is revealing the picture, he takes it out of the revealer and exposes it to light, without the picture being submerged in fixer. A picture that has not been in fixer will start blackening instantly by the light. He treated the photo as though the whole process had been completed.
(at around 1h 13 mins) When the priest is telling them about the graveyard and how to get there, he describes it as an old cemetery from Etruscan times. But when they get there, it is obvious that the cemetery is far more contemporary than the Etruscan Civilization.
(at around 1h 19 mins) The engraving on the child's grave has some mistakes. The first two words are Insantem Masculum. The first word should actually be Infantem. The last line (Faecula Comtlectum" is supposed to mean "The generations embrace" but is just gibberish.
(at around 1 min) In the first scene when Robert Thorne is being driven through Rome, the time is specified onscreen as 6.00AM and the date is June 6th. The sun rises in Rome at around 5.30am at that time of year, which means it should be light outside, but Robert is being driven in the dark.
(at around 1h 2 mins) Jennings shows a picture he had mistakenly taken of his own reflection in the mirror at the priest's apartment. In the photograph, however, he is clearly not pointing the camera at himself.
31:39 Ambassador Robert Thorn says they killed his child as soon as he was born, but the child skeleton from the old grave was too big and well developed for a newly born baby.
(at around 44 mins) The guide wire can be seen on the pole that falls from the church.
(at around 51 mins) When Mrs Thorn falls from the railing and she has landed on the floor below, Damien can be seen peering through the railings with only his head poking through them. This shot is from below. When the shot is changed his hands are now grasping the railings as he peers down.
(at around 1h 35 mins) When Mr. Thorne is in Damien's room with the scissors while he is asleep, you can see Damien's eyes blink.
When Father Brennan tells the poem to Robert Thorn, he does not say that the poem comes from the Book of Revelation, merely that it was predicted in the Book of Revelation.
(at around 1h 21 mins) When Thorne and Jennings are being chased through the graveyard by the Rotweillers, you can make out the dog handlers for a brief second behind some bushes.
(at around 1h 26 mins) Toward the end of the film, Jennings says that the place name Megiddo derives from the term Armageddon. Actually, it is the other way around - "Armageddon" is a bastardization of "Har Megiddo", which, in Hebrew, means simply "mountain of Megiddo". According to Revelation 16:16, this would be the site of the last battle in history.
Numerous characters, but most notably priests, refer to the book in the Bible as "Revelations" (plural) when in fact, it's proper name is the "Book of Revelation," or "The Revelation to John," singular. Any educated professional clergy member would know it's correct name.
(at around 1h 27 mins) Keith Jennings, the photographer, says that Megiddo is 60 miles south of Jerusalem. In fact, it is north of Jerusalem, 22 miles north of Shechem and 15 miles south of Haifa.
(at around 24 mins) When Mrs Thorne says she wants to take Damien to the wedding, Mrs Baylock says that a 5 year old wouldn't understand the goings-on at an Episcopal wedding. But since she's a Brit, and they're in England wouldn't it be Anglican? The Episcopal Church is called that in the USA. In England, it is the Anglican Church.
When Robert and Jennings find the graves in the old cemetery in Cervet, Robert reads the gravestone of what would be his son's grave as "Bambino Scianna" (translation: Baby (boy) Scianna). But the gravestone doesn't actually say that.