In shots of the seaplane near the island you can see the struts of the landing gear indicating that the gear is extended to the down position. However, in a water landing the wheels would remain retracted. The wheels would only be extended if they planned on taxing the plane up a ramp onto dry land.
When Matrix jumps from the landing gear of the plane, he lands in water and gets his trousers and some of his jacket wet. Although he takes his jacket off, in the next scenes, his trousers are completely dry again, only a minute or so after getting out of the swamp.
When Matrix is raiding the surplus store, and enters the hidden room full of guns, he grabs the rocket launcher off the wall and hands it to Cindy. After he says "Go!" and she leaves the room with the rocket launcher, the next shot of Matrix shows it hanging on the wall again.
After Matrix tears the passenger seat out of Cindy's car and gets inside, the car door window is clearly visible, but in the following shot where Cindy pulls out of the parking space, the window is down.
During the big shoot-out near the end of the film, Matrix is using an M-60 machine gun which repeatedly acquires more ammo (the ammo belt is replenished) even though Matrix has no spare ammo with him, nor any time to reload.
When Matrix is "shopping" he puts many guns in the cart but he grabs the pistol and the shotgun shells after he tells Cindy to leave with the cart. Then he is arrested and the weapons that he grabbed after Cindy left are obviously confiscated, yet when he suits up on the beach for battle the pistol is one of the weapons he has and during the shootout the shotgun is fully loaded.
Shortly before Matrix enters the mall, we can see a white pick-up truck and a grey Renault LeCar stuck in the traffic. At this time, the right headlight and the front bumper on the LeCar were broken. During the chase scene, shortly after leaving the mall, we can see both cars again. Except that the car has been fixed.
When Matrix gets captured at the beginning of the movie the M-16's shoved into his chest by the baddies have the old-style three prong flash suppressor on the barrel. After Bennett reveals himself, a newer A1 flash suppressor (well, newer for that time anyway) is shown.
At the beginning of the movie when Arius' henchmen shoot at Matrix's home, Matrix has a cut on the side of his forehead which keeps appearing and disappearing in between shots while he's talking to Kirby's soldier, Jackson.
During the fight scene with Cooke in the Motel room, Matrix grabs Cooke's arm with the gun and rams it through the glass panes by the shower. While doing this, they knock down the lampshade, which miraculously reappears in the next scene.
When Matrix arrives on the island and exits the dinghy in the water before pulling it ashore, you can see that he has white swimming trunks on which magically turn black in the next scene (4.3 version is better as the screen appears closer).
When Matrix arrives at the airport, Bennett is in a Mercedes. The passenger door can be seen to have no rain guard along the top. When Matrix sticks his head in the door to talk to Bennett, a rain guard is clearly visible. As Matrix walks away, the rain guard has disappeared.
When Matrix is viewing the barracks with his binoculars, he is seen moving the binoculars from right to left. However, when the view switches to show through the binoculars, they are clearly moving from left to right.
Just before Bennett breaks through the door of Jenny's holding cell, you can see about 40 yards up the corridor, which is empty. However as soon as he breaks through the door barely a second later, a group of soldiers run past the door from right to left.
As Matrix exits the shed and picks up the M60 machine gun, he fires at infantry to the right of him. In the next scene, a close up of Matrix's torso, shows a strap across his chest which was not there when he exited the shed.
When Sully buys the passports in the mall restaurant, he puts them in his pocket, but when he leaves to see whats happening outside in the mall the bag with the passports are clearly sitting on the table.
Right after Matrix and Henriques take their seats on the plane, the orange curtain behind Matrix switches from closed to open between shots. Shortly after that, as the fly hostess closes the curtain, she repeats the same movement twice.
When Matrix is gearing up to go and find Jenny, he paints his arms and face with camouflage paint and then puts on his combat vest and you see his chest is unpainted. Yet later on when he gets caught in the grenade blast and takes it off, his chest is painted.
After Matrix is merely scratched by a grenade and seeks refuge in the tool shed, He comes out with the machete and ax in each hand correctly, yet when he swings the ax up into the soldier's groin it is in his hand with a reversed grip.
Immediately following the kidnapping of his daughter, Matrix is confronted by the thug who tells him he must cooperate if he wishes his daughter to be returned. Matrix is holding a G3 assault rifle, but when he shoots the thug it is clearly a pump action shotgun in his hand. In the next shot Matrix is holding the G3 again.
At the end, when the helicopters and the sea plane land at the beach, you can see a cruise ship in the background in a wide shot. A later wide shot shows the pier and open sea, but no ship. Then in a final shot, you see the pier and the cruise ship.
When Matrix bulldozes the entrance to the surplus store, there is debris blocking the entrance. Cindy needs to step over this debris on her way, yet is able to roll a shopping cart full of weapons and ammo out the same path on her way out.
When Matrix begins his decent in the Blazer the front grill is a 3 bar black insert and the truck has black 4 wheel drive front hubs. A second Blazer is used during the shoot but has a basic gray grill, white front hubs and much smaller front tires.
When Matrix escapes from the aircraft during take-off, he leaves doors open and breaks down sealed curtains. This would set off alarms in the cockpit and leave the aircraft unpressurized in flight; and therefore unable to complete an 11hr flight.
When Matrix is following the kidnappers with his sabotaged truck he goes down the forest in a straight line. The guys he's chasing use the road, which has several turns. He would actually overtake them after the second turn. Yet every time we seem him he is about the same distance away from the cars he's chasing.
When Matrix crashes his car while chasing Sully, neither Matrix nor Cindy are affected by the crash even though neither are wearing seat belts (Cindy isn't even in a seat!), and the crash was powerful enough to severely damage the front end.
When Matrix gets his weapons from the shed during the attack that ends with his daughter being kidnapped, we see him pull back the loading handle on his rifle - however, the weapon is a Heckler & Koch HK91 which fires from a closed bolt, meaning that to make it ready to fire you actually have to slap the cocking handle into the forward position (after inserting a loaded magazine). Note: It's the same action you see Keanu Reeves perform on a H&K MP5K submachine gun (basically the compact submachine gun version of the H&K rifle) during the "lots of guns" scene in... The Matrix (1999).
The red car was chasing the Porsche. The Porsche was destroyed on the driver side when it was flipped in the accident. When Arnold took off in the Porsche after he turned it right side up, the car was perfect.
In the fight scene in the motel room, Matrix grabs Cooke's arm and forces it through the glass tiling in the bathroom. The tiles wobble and fall away without resistance and in a closer shot you can see that there is no cement or other bonding material holding the individual tiles together.
When Matrix swings across the mall, his face is obscured by his arms. However you briefly see the stuntman's face as he lands, before the camera cuts to show Matrix preparing to jump from the top of the elevator. In the meantime you can clearly see the stunt man's wig fly up when he lands on the elevator;
When Matrix and Cindy are about to take off in the plane, the daylight varies: when they are filmed from outside it's about to get dark, from inside it's the middle of the night and then it's about to get dark again.
When Matrix and Cindy are flying towards the island and are discovered by the coast guard they dive towards surface to avoid radars; you can see the pitch changes - yet the vertical speed indicator is in a neutral position, indicating no dive at all.
In the fight between Matrix and Arius, Matrix rolls out and fires his shotgun repeatedly at Arius leaving blood stained bullet-holes scattered randomly all over Arius' chest. As Arius falls towards the window, the bullet holes can be seen all lined up in little sets of six.
In the final battle between Matrix and Bennett, Matrix is holding his knife in his right hand. However, when Bennett pins Matrix against the wall, Matrix manages to somehow switch his knife from his right hand to his left hand.
At the end of the film, we see Cindy beach the plane with the nose of the aircraft facing the camera. After the dialogue between General Kirby and Matrix, Matrix and Jenny go to board the plane which is now facing in the opposite direction.
Shortly before Matrix kills Arius, he fires his assault weapon through multiple glass window panes, shattering most. However, no parts of the window frames are damaged, although when Matrix next jumps through the shattered windows, it is clearly seen that the frames are made of wood or an easily breakable material. It would be impossible for Matrix's bullets to have hit the glass windows only with no damage to the delicate framing around them.
In the end when Matrix is fighting with Bennett, When Bennett is hitting Matrix with a metal pole, the metal pole is a very obvious rubber prop, because the metal pole bends when Bennett is hitting Matrix.
Before the final shootout, Matrix plants explosives on the edge and around the different buildings, yet when he detonates them, the explosions clearly come from the insides of the building (and the top of one of the watchtowers).