The number of Roman guards searching the PFJ headquarters changes as they enter and leave the house.
When the gladiator has a heart attack in front of the entrance gate to the arena, a high ranked Roman then makes the comment absolutely dreadful. Next scene the gladiator is no longer in front of the entrance gate.
When the Centurion corrects Brian's slogan, "Romanes Eunt Domus", he says Domum is the locative case, which would be Domi. It's actually the accusative of place, which drops the preposition Ad from Ad Domum. However, the resulting sentence, "Romani Ite Domum", is correct.
During the crucifixion scene, after the PFJ sings "For He's a Jolly Good Fellow", a very obvious double for John Cleese is playing "Reg" among the PFJ when Cleese enters the scene as the Centurion, looking to free Brian.
The prisoners carry crosses considerably smaller than the ones they end up being crucified upon.
In the manger scene, John Cleese has obvious lines on his face where his make-up has run from sweat.
When Brian falls off the balcony and knocks the prophet into a large jar, he is clearly hanging on a bar with his hands.
The letter U first appeared around the 14th century. At the time of Jesus, ROMANES EUNT DOMUS would be written ROMANES EVNT DOMVS.
When a nude Brian speaks with his followers and his mother storms into the room, a Star of David is on the wall. The Star of David became a symbol of Judaism in the Middle Ages.
When the Suicide Squad arrives during the crucifixion scene, Otto's first line is clearly dubbed. An earlier scene featuring the Suicide Squad was cut, so Michael Palin needed a different line to introduce them.
During "Always Look on the Bright Side of Life," when the camera looks down the line of crosses, a man in a suit and tie walks in the background.
When the three wise men praise Brian, an electrical extension cord is clearly visible, hanging down on the right of the screen (widescreen).
Around the 43 minute mark you can briefly see one of the crew underneath the alien puppets (the one on the right) when both aliens jump up as the ship comes under attack.
After Brian had his speech and the people pursue him asking him to complete his sentence, there is a frontal shot where the cameraman's shadow is visible on the crowd and Brian.
When the crowd of people following Brian claim he is performing miracles, a blind man says he is healed. A stunt mat is visible when he falls into the hole.
When Brian's mother buys rocks for the stoning, the boom mic is visible at the top of the screen, swinging from side to side.
When the priest starts reading out the name of the person to be stoned, the shadow of a boom mic is visible on the wall behind him.