In the beginning of the film, when they discover the Mona Lisa, the picture is actually several times larger than the real Mona Lisa, even though the scan shows that this is the authentic one. A canvas of the Mona Lisa is identified being "authentic" by a scanner. The real Mona Lisa is also painted on a poplar panel about an inch thick, not a canvas as shown in the movie.
When the dogs are being executed, the soldier carrying out the executions is holding a Walther WA2000 sniper rifle, but there is a the sound of a pump-action shotgun preceding each shot. The soldier carrying the weapon is not seen "pumping" the weapon.
After the raid on a sense offender's hideout, Preston takes off his gloves and touches a wall, during which he finds a bullet hole which reveals a stream of light coming through, hinting a hidden room on the other side. However, when he enters this room, no lights are on and it is pitch black.
As the clerics raid the sense offenders' hide out, Preston removes his gloves and drops them. A few shots later he takes them off again, and when he gets home he is once again seen taking off his gloves to take the prozium.
At the beginning of the movie, when Preston and Partridge return to the city Preston comments about returning to the city, Partridge says "It does?" with high inflection on last syllable as if asking a question, to then repeat himself more confidently after dosing himself, "It does". When Preston is later reviewing the video of that interaction, the video replay shows Partridge initially saying "Does it?". The playback of the first quote has the two words reversed.
When Preston takes the Dog out to the Nether, he uses his keys to open the trunk and we hear the jingle, but when he gets back in the car, the keys are in the ignition still. (when he gets back out of the car he takes his keys and uses them to open the trunk)
When Preston shows the picture of Partridge to Mary, the picture is shown lying on the table as he walks out of the room. In the next shot, he is sitting at his desk looking at the picture, even though he left it behind.
The condition of the picture of Errol and Mary changes from the interrogation room to the scene of Preston at his desk. When Preston shows the picture to Mary it's wrinkled and creased, but one scene later the picture is in a like new condition.
In the pistol whipping sequence, when you see Preston's pistol in slow motion about to hit a guard's faceplate, you can see the reflection of Preston moving to hit the visor itself. The reflection shows Preston hitting with his left hand, but when the real hand shows up, it is actually his right hand.
When the troops pull up to Preston in the Nethers, the lead motorcycles can be seen leaning to the right (screen left) on their kickstands. When Preston does his backward somersault off the middle bike, it's parked straight up and down and the fairing is missing.
In the pistol whipping sequence, two sets of spikes come out of the magazines. When you see Preston's pistol in slow motion about to hit a guards faceplate, there are no spikes present. Also you can clearly see that it is a stuntman in the reflection of the visor.
In the car where Preston asks Partridge about the book he's bringing back, Partridge pulls it from his pocket it is a thin poetry book. Later when Preston finds Partridge, reading the same book, it is 3-4 times thicker than the previous one.
When Preston fights the bodyguards with the swords, he impales the last bodyguard through the chest and the sword protrudes out of his back. However, when the bodyguard collapses, the end of the sword is gone and his back appears completely untouched.
During the scene in which Brandt picks up Preston at the distribution center, the wheels on the Seville change from the custom five spoke alloys to the standard Cadillac wheel for that particular model, and then back again.
When the two guards step through the double doors into the hallway in the final guard shootout scene, the one on the left of the screen steps past the door handle but when the shot cuts to another angle they are scene catching their arm on the door handle and pulling their arm out of the way.
Double-doors entering the round room with Father at the end of the movie show mismatched locks and latches. One door shows an edge surface with deadbolts and catches as expected, but the other door has a smooth plain surface with no striker plates or any other hardware suitable for matching the first door's latches.
At the end of the film Preston is seen holding the red ribbon in his right hand. Just prior to this his right hand is covered in blood when he wipes it down the screen. When he is holding the ribbon both it and his hand are clean.
In the final shoot out where Preston is fighting the guards in the hallway, he releases the clips out of his guns and new clips come out of his sleeves. The clips that are inserted into the gun are the regular clips he uses, but in the next shot when he begins shooting the clips are obviously the round bottom ones.
When Preston slides the 2 clips down the corridor, there are two guards running down the hall toward the clips and you can see one of the guards start to jump over them. In the next shot, the clips slide right up to the guard's feet.
As Preston gets back into his car after dropping off the puppy in the Nethers, exhaust vapor is visible behind the car (i.e. the engine is running). A moment later, he starts the car (again). Additionally, the exhaust vapor is going back into the pipe.
During the flashback to Viviana Preston's arrest, when John twists the soldier's wrist to take his weapon the gun is an AR-15/M-16, but it then appears to instantly change to a Beretta AR-70 as he holds it on another guard - actually, this is not a continuity error; Preston first disarms a guard of his AR-15 type rifle (by breaking his fingers), then uses that rifle to deflect the weapon of another guard, whose AR-70 he grabs and turns on its owner (it's not possible to see which kind of rifle he uses during the lightning-quick deflect maneuver).
A weapons analysis when Brandt arrests Preston for sense offense shows that it was Brandt's firearm that was used in the slaughter of the patrol in the Nethers (when Preston attempts to release the puppy); however, the scene in which Preston slaughters the patrol happens approximately 12 minutes before the scene in the film in which he switches guns with the oblivious Brandt. Preston's line at the supposed moment of the firearm switch is referenced during the arrest scene when the "switch" is revealed to the audience, confirming that it is the time at which the "switch" is considered to have happened; however, if this is the case, Preston could not possibly have had Brandt's gun when he was confronted by the patrol in the Nethers. There is the auxiliary issue that Preston used two pistols in his slaughter of the patrols, meaning that at least one of the guns should still have been matched to Preston.
When Preston fights the bodyguards with the swords, as he kills the last two men you can see that the man behind him (whom Preston just stuck a sword through) doesn't hold the first part of the sword in a straight line, but accidentally holds it in an angle as he collapses.
In the katana fight Preston jabs into one of the men, and it's clearly visible the sword misses the torso, and the actor's actually holding it between his arm and against his chest. In normal playback the move looks nevertheless convincing.
The goof items below may give away important plot points.
When Preston shoots the final two helmeted guards in the room where he was having his emotions monitored during Father/DuPont's speech, there are three muzzle flashes but the sound of four shots being fired.
In the fight in the hall outside of DuPont's office, when Preston throws the two gyroclips into the hall and kills the two running guards, the standing guards raise their weapons to fire upon Preston. However, in the wider shot when you see the two dead guards dropping to the ground, all the guards still have their weapons at their sides.
During the fight outside DuPont's office, John Preston drops his two pistols (at the end of the hallway fight) and is running up to the assault rifle (the one he flips over his head). As he is running up to body and the rifle, you see the guards running up to the door. Just before the the camera angle switches to the rifle, you see the guard on Preston's right stop and take aim. After Preston gets the rifle and takes aim, it cuts back to the two guards and you yet again see the guard on the right running up to the door and get shot down.
At the beginning of the scene where Preston shoots Partridge, Preston puts both his hands before his waist, holding his gun with his left arm and his right is empty. Later he shoots Partridge with a gun in his right arm, though we never see a motion of him swapping the gun, and later his left is empty, indicating he didn't pull out another gun.
When Preston fights the guards outside Father's room, after dispatching the two first guards, he stands to look at the rest of the guards in the hallway. In the next shot, the bullet holes made by the two first guards have disappeared from the wall behind Preston.
Partridge is shot in the face and yet when Preston sees his body in the morgue, there is no bullet wound in his head. Partridge is actually shot in the neck, the bullet wound is visible in the morgue on his neck.
When DuPont is revealing to Preston that Father's visage has been used as a political puppet some 'cut and paste' work becomes apparent. The words in the speech "The council simply elected me..." and "...to pursue his paternal tradition" appear to be from different shoots as DuPont's face snaps from one frame to the next to a different position and the tense in his voice dramatically shifts.