Jericho raves at Satan that he is not as evil as Jericho is. Jericho says "You think you 'know bad', eh? Well, you're a fucking choir boy compared to me! A Choir Boy!" instead of the scripted line "You're Choir Boy!"
After the priests have tried to kill Christine at her home, Jericho is seen walking behind her. One shot the white door behind is open but when the frame changes to Jericho the door is shut and then back open in the next shot.
When Jericho follows the priest through the door in Saint John's church, there is a stairwell behind it turning to the left, leading into the basement. Yet moments before, when we see the door from the other side, it leads into a room on the right. Also, in these two shots, the door opens to different sides.
When Bobby surprisingly returns after having been burned to death earlier in the explosion/fire of his vehicle, no singe or scorch marks are seen on his clothing, despite having been surrounded by intense flame. Although he did make a deal with the Devil, it was Bobby with whom the Devil made the deal, not his clothes, which should have been burned off in the fire or show some evidence of the extreme fire and heat they'd been subjected to.
When Jericho jumps on one of the Knights in Christine's bedroom, he knocks a panel out of the open door next to her bed. In the next scene where he is talking with her about her past, the panel has been replaced and the door is shut, but is open again in the next shot.
In talking about the End of Days, Father John says that the Gregorian Monks created the Gregorian Calendar in order to be able to correctly identify when the Apocalypse was going to happen (1999). In reality, there is no such monastic order as the Gregorian Monks. The Gregorian calendar was actually named for Pope Gregory XIII, who was Pope when the calendar was first implemented in 1582. The calendar was adopted because the old Julian calendar was slightly too long, and the date of Easter was slowly drifting forward.
A voice-over news announcer reports that blood has been seen coming from the hands of the infant Christ child in the sculpture "The Pieta". However, "The Pieta" does not depict the infant Jesus - it is a statue of Mary holding the dead body of the adult Jesus.
One of the symbols leading Satan (Gabriel Byrne) to his subjects is a pentagram with three of its arms facing upwards. A pentagram with three of its arms facing upwards is *not* a symbol of Satanism. It is a symbol of the Wiccan faith, and Wiccans do not believe in the Devil. A pentagram with two of its arms facing upwards and the other three facing downwards is a symbol of Satanism.
Much importance is attributed to the date being exactly 2000 years since Christ's birth. The exact year is unknown, and even the best historians admit that the Roman calendar (which was established many years after Christ's death) is probably off by more than 10 years. However, one of the clerics in the movie 'reveals' that in the movie's universe, the Gregorian calendar was actually set up by the Catholic church so as to let Satan's return occur at the turn of the millennium.
Although we see Satan move into a new body in the film, he goes to great lengths to protect his current one. This is because he's put a lot of effort into this one - he tells Christina that this is the face she's seen all her life, for instance.
It is said that the Mark of the Beast is "666" but in Apocalypse it was to be inverted, so the real Mark is "999". In the time of St. John number "6" was not in use; it is an Arabic sign and came to use several centuries later.
The goof item below may give away important plot points.
Incorrectly regarded as goofs
In the final sequence when Satan has over taken Jericho's body, you can hear Jericho screaming for "Christina" to come out of hiding. The character's name is "Christine" not "Christina". However, in German (Arnold's native language), an E at the end of a word is pronounced like an A in English.