In the car chase with the Wet Nellie (just before it runs into the ocean and transforms into a sub) the helicopter can be seen firing its machine guns directly into the ground, but there are no impact plumes or sound effects as in previous scenes.
Bond honks the horn on the Wet Nellie before passing a truck on the cliff side road. Bond presses the center of the steering wheel when a Lotus horn is actually the lever on the left of the steering wheel.
When escaping from the Liparus by firing a torpedo at the bows, the captain gives the standard order; "Match bearings and shoot". But in this case they are not tracking a target, so there are no bearings involved; they are shooting straight ahead.
In the opening credits, the last girl who is doing flips supposedly on the end of the gun barrel pulls down the actual bar during rotation to the point where it shows under the gun barrel (blue; during director credit).
As Bond and Triple X are rising to the surface in Stromberg's escape pod, the pod is shown with a long appendage extending down from the bottom of the craft. When the British surface ship opens it's stern door the pod floats into the cargo hold upright which it could not do with that appendage.
When Bond first looks for Fekkesh, he enters his house with a buttoned jacket. He is met by a woman. Bond then looks away, the camera catches him from behind. When Bond turns around, his jacket is unbuttoned. We never see him unbuttoning it.
On the globe in the control room of the Liparus, both submarines as well as the Liparus are shown being in the Atlantic ocean. Stromberg and Anya could never have made it to "Atlantis" (which is supposed to be somewhere near Sardinia) in time, using the small escape vessel. Even at full speed it would also have taken several days for the USS Wayne to reach 'Atlantis' when there would be plenty of NATO forces much closer.
They travel from Cairo to Sardinia by overnight sleeper train. Not impossible, provided you're happy to go through Sinai, Israel, Lebanon, Turkey, across the Bosphorus, through Greece, the former Yugoslavia, down Italy and then catch a ferry. Or alternatively through Libya, Tunisia and across the Med. But, since they're trying to avert nuclear armageddon, flying might be a bit quicker.
When the USS Wayne is tracking the Liparus, the captain ranges it at 6,200 yards. Then approximately one minute later, with no obvious time skip, the Liparus is immediately behind the Wayne and captures it. Closing 6,200 yards in 1 minute puts the Liparus' speed at 211 mph, a speed no ship of that size could ever reach. So when the captain utters "impossible", he's right.
When Bond and Jaws are fighting on the train, he breaks a lamp, and uses the live wires to "electrocute" Jaws. Since Bond and Jaws are struggling and their bodies are making contact, Bond would get shocked equally as much as Jaws does.
On Major Anya Amasova's shoulder rank boards there is a star and a single red stripe in the middle. The rank board of a Soviet Army Major is supposed to have a star between two stripes running along the length of the board.
It's obviously a joke, but... as Bond drives the Wet Nellie out of the sea, he hands a fish to a person on the beach. If there was a hole large enough to allow a fish to enter the car/submarine, they would surely have drowned, or at least got very wet (although a leak did occur in the roof of the car just before it emerged from the water).
The Lotus goes underwater, and "transforms" into a submarine. The bottom of the car changes without explanation. The tires get pulled in, they are each replaced by a completely flat white panel. It cuts to another shot where the panels are not flat at all, but have retractable "fins." It also becomes clear there would not have been room enough for both the tires and the retractable fins in the same wheel well.
Bond and Major Amasova arrive at Atlantis by boat, approaching (obviously) at sea level. When Bond goes to see Stromberg, Naomi tells him to press the third button and the elevator takes Bond upwards. Yet when he steps into Stromberg's lair, the views out of the windows show fish swimming around, and in some cases show the sea bed, even though the room is apparently tens of feet above sea level.
At around 19 minutes, when the helicopter carrying Dr Beckmann and Prof. Markovitz away from Stromberg's Atlantis is blown up, the wreckage falls onto a solid surface in the middle of the sea. There is no splash.
In the ski chase at the beginning, right before James Bond goes over the cliff, the long shot shows a gentle slope to the edge. Then the closeup scene cuts to a steep dropoff which wasn't seen in the long shot. In addition, as he skis down to the edge you can see ski tracks which are obviously from previous takes.
The goof items below may give away important plot points.
As the Liparus is exploding around them, the captain of the American submarine gives the order to load the torpedo tube with a Mark-46 torpedo when he should have said "Mark-48". The Mark-46 is about 10 feet shorter than the torpedo seen being launched in the film.
When 007 returns to Atlantis to rescue Anya; after he first arrives on the dock, he is asked by Stromberg to board an elevator. As the elevator starts upward, for a split second a member of the crew appears to be walking on a walkway behind the open metal shutters to the left of the elevator shaft. And a split second later his shadow is visible.
When the two nuclear submarines are programmed to destroy each other, it has blips of the missiles being launched on the globe map. They travel a curved path on the map. If these missiles were traveling the shortest path, then they would appear to travel a straight line on the map, otherwise if this was the path of travel then they would be going thousands of miles out of the way and wasting tons of fuel. This is most likely because the blips on the map are incorrectly represented as if from a side-view perspective rather than an overhead perspective.
When Bond fights Jaws on Atlantis, his Walter PPK pistol runs out of ammunition, he reloads it and fires again. Some scenes later on, he picks it up and arms it. But in the previous scene he has fired it once after reloading so the pistol is obviously already armed. Besides being totally unnecessary to arm it again, the bullet already in the chamber should be thrown out to the right as a result.
Bond's trusty Walther PPK is a "double action/single action" pistol. The first shot cocks the hammer automatically for the second and subsequent shots. When Bond kills Stromberg, he fires two consecutive shots, both double action, and with no flash from the gun.
XXX says that she had stolen the plans for the Wet Nellie. She seems astonished when they first dive into the water in it, but since she had not had any indication that this was anything but an ordinary car, she would not yet have recognized it for what it was.
The man who leads the assault on the control room and gets killed can be seen alive later entering the submarine. When James Bond is captured and brought to the control room, the guard behind James is clearly one of the scientists from the beginning who are killed in the helicopter.
In the phone booth, Jaws supposedly bites a man to death. If you look closely, Jaws does not even bite the man. He makes the motion like he's about to bite him, but the man faints before he gets the chance. He doesn't break skin or draw blood or anything. Yet, the man dies from being "bitten" by Jaws.
When the USS Wayne fires its torpedoes at Atlantis, their blue color is clearly visible. Blue colored torpedoes are merely training inert rounds with no warheads. They could not possibly do any damage to Atlantis.