Plot hole: Why on earth do they drive the Minis up the ramps into the bus while it is moving? They are on a long, straight, relatively quiet stretch of road, but there are cars and buildings about. That ramp is going to make a noise like the sky coming down (we see sparks as it scrapes on the road) and they put on a display anyone would be, frankly, amazed to see. Don't they think one single person would call the police? Don't they think that reports of three brightly coloured Minis will be connected with the recent robbery? They cannot possibly think they have to load the Minis on the run in order to elude the police; they have lost the police cars and are no longer being pursued. Why not just park the bus on the hard shoulder and drive the Minis sedately up that ramp? An unusual sight, maybe, but nowhere near as clumsy, obvious and attention-getting as the way they do it. They are asking to be pulled over and arrested.
Plot hole: Blofeld tells Bond that he realised he was not the real Sir Hilary Bray when Bond told him that the Bleuchamp tombs are in the Augsburg Cathedral. Blofeld informs Bond that they are in-fact in the Saint Anna Kirche, and the real Sir Hilary Bray would've known this. However Bond had gotten his information about the Bleuchamp tombs in Augsburg from the real Sir Hilary Bray earlier in the film. (01:19:05)
Plot hole: At the very beginning, as the passenger ship is foundering in a powerful storm, the little boy places his kitten in a box and tucks the box inside his shirt just moments before he is cast into the churning sea. Sinking into the depths, the boy and other passengers are presently rescued by Captain Nemo's team of divers, who supply the drowning passengers with oxygen until they board the submarine Nautilus. Once aboard, the little boy opens his hidden box to reveal a wet but very much alive kitten that could not possibly have survived submersion for that length of time in a box that was not waterproof.Charles Austin Miller