Plot hole: While it is essential to the story, there is a problem with apes in the space ship. While it is the one that took Taylor to the future, there is no way the chimps could have salvaged the ship from the water (plus there wasn't enough time for such a salvage operation. Kira and Cornelius were living in the ape city we see in "Beneath the Planet of the Apes" never mentioning to Brent that they found a spaceship he could travel back with). They didn't have the technology for such an operation, no diving suits, and chimps are scared of water. Also, the water would have destroyed the power systems of the ship when it sank. (00:00:25)
Plot hole: When Saxby tells Blofeld to watch Peter Franks on the CCTV, Blofeld would have recognised him as James Bond. Why does Blofeld keep quiet about it? What possible use could he have for catching, rather than killing, Bond? (00:38:34)
Plot hole: The sergeant tells Stone that he only has to listen for a bell for an important communication coming through and will then alert the rest of Wildfire. Yet later, Dutton notices a message already printed out. So at a facility this important, the sergeant just ignores the machine if it prints out a message and doesn't ring? He has to have clearance to read them or they wouldn't print out where he is. It's a bit too convenient for the plot that he wouldn't visually check each message to make sure.