Continuity mistake: In the final fight scene on the plane between Jinx and Agent Frost, Jinx is slashed across her stomach, drawing blood. In a later scene, when Jinx and 007 are pouring diamonds over one another in the hut on the cliff, her stomach is unblemished. (02:02:25)
Continuity mistake: The T-Bird following Oddjob to the junkyard does not have fender skirts but does when they give up the chase and head back to the farm. (01:16:25 - 01:20:30)
Plot hole: Necros had absolutely no way of knowing that Bond and Saunders had arranged to meet at the cafe when they did, and wouldn't have had anywhere near enough time to track them down and set up his elaborate booby trap. Saunders only suggested the meeting place and time a few hours earlier, and it was kept strictly between him and Bond. The scene in Tangier where Whittaker tells Necros to kill another British agent takes place on the same day Bond arrived in Vienna; meaning that Necros got from Tangier to Vienna (a 5 hour-plus flight), tracked down Saunders, acquired the materials to booby trap the cafe doors (or had planned this ahead of time - unlikely) and set the trap up well in advance of he and Bond getting to the fairground. There was nowhere near enough time for all of that to happen without Necros having psychic knowledge of Saunders' movements.
Other mistake: When the Disco Volante separates to escape the cruisers firing on it, the "cocoon" is seen facing the pursuing ships stern first. When the shot changes to show the gunners firing on the ships the back half of the "cocoon" has turned completely around; the gunners are firing from the separated mid section of the Volante and the stern of the "cocoon" is now facing away from the cruisers, making it easy to see which parts of the scene were filmed live and which were done in the studio.
Continuity mistake: In a scene towards the end of the movie where Bond and Vesper are lying on the beach, Bond has sand on his back through most of the scene. When they start to kiss, in the distant shot towards the end of the scene, he has no sand on his back at all. (01:57:10)
Revealing mistake: During the fight scene in the belly dancer's room, Bond spins the bald guy around to avoid being hit by a chair. When the bald guy gets hit in the back with the chair, you can see a large rectangle of padding under his jacket.
Continuity mistake: When Bond escapes from the Willard Whyte facility in the desert in the moon buggy, a car that is chasing him goes over a ridge and turns on its side as the buggy speeds by. A wheel rolls back into the shot, all on its own. It doesn't belong to the car, or the three three wheelers also chasing, but looks like it belongs to the buggy, which has its full compliment of wheels all through the scene.
Plot hole: In the final showdown, when Bond is fighting with Stamper, the girl is wrapped in a chain hanging from a crane and dropped in the sea. After the boat blows to bits, the chain continues to hang down even though there's nothing holding it. It even keeps hanging after Bond's swum down to untie her. What's keeping it there? Do all stealth battleships come with buoyant chains? With both arms at least partially free, why doesn't she just climb back up the chain?
Continuity mistake: Just after Bond and Christmas Jones climb out of the pipe, Bond is holding his shoulder and his blazer sleeves are up. In the next shot, his arms are by his side and his blazer is all neat. (01:20:05)
Factual error: During the boat chase scene, Bond throws a grappling hook/anchor from the old boat he is driving onto the deck of the rubber boat "riding" his. The rubber boat is then violently yanked off of Bond's boat and crashes. This makes no sense. For the rubber boat to be yanked off that way, the other end of the anchor line would have to be tied to something stationary. However, the other end of the line is just lying in Bond's boat. There's even a shot of it sitting there.
Factual error: When Bond is involved in a high-speed chase on the way to Miss Taro's house, his wheels are squealing like crazy, but he's on a dirt road. (00:48:10)
Continuity mistake: The train is stopped because Spectre has pushed a 1950's style Dodge truck full of flowers in the trains path. Later, when James is driving it trying to avoid the grenades dropped from a helicopter, the truck has turned into a very different looking 1961 Chevrolet truck.
Deliberate mistake: Blofeld doesn't recognize James Bond in this film, even though they met face-to-face in the previous movie, "You Only Live Twice." There is a production-related reason for this. Ian Fleming wrote "On Her Majesty's Secret Service" in 1963 (in which Bond and Blofeld met for the first time), and he wrote "You Only Live Twice" in 1964. However, "You Only Live Twice" was adapted for film first (in 1967), and "On Her Majesty's Secret Service" was adapted afterward (in 1969). Because the 1969 film was so faithful to its source material, Blofeld and Bond are basically meeting for the first time...again. The producers were aware of this continuity problem and intended to have James Bond undergo plastic surgery for "On Her Majesty's Secret Service" (which would conveniently explain Blofeld not recognizing him, as well as the fact that Sean Connery had been replaced by George Lazenby in the lead role). But the plastic surgery idea was discarded in faithfulness to the novel, resulting in a glaring continuity problem between the 1967 and 1969 films.
Plot hole: Bond makes a huge tactical error after diving to the St. Georges. He knows the Russians and their operatives are after the ATAC. The ATAC itself is expendable to Britain, since it has a self-destruct mechanism that under proper procedure would have been set off when the ship sank. So why is Bond trying to retrieve it? Because he disarms the self-destruct, he actually allows Kristatos to get his hands on it, forcing Bond to track it down again and, to stop the Russians from getting it, HE DESTROYS IT! So why doesn't Bond, instead of disarming the self destruct, set a timed charge or toss a grenade in the room to destroy the ATAC while it's at the bottom of the sea? The answer is, of course, that if Bond destroys the ATAC before the bad guys can get at it, the movie's over. Even so, at the end, when Bond finally does destroy the ATAC, he tells Gogol it's "detente. You don't have it. I don't have it." Clever line, but it reinforces the fact that the British don't need it. They can build another one.