When Ned sees the giant squid starting to sink and taking Nemo with it, he draws his knife from his belt and dives in to save Nemo. Arriving at Nemo's position, the knife is back in his belt and needs to be drawn again.
When they wait outside Roa Pandi for the sailing ship to leave harbor, the Nautilus is seen floating closely to the island. When Cpt. Nemo orders Full speed ahead in a subsequent shot, the Nautilus is shown at open sea.
Shortly after first entering the Nautilus, Ned, Professor Arronax and Conseil watch a submarine funeral service taking place on the ocean floor. Considering the Nautilus is at the surface at the time yet is only ten feet or so above the ocean floor, this makes the water unrealistically shallow for the middle of the ocean.
The film opens on what purports to be a copy of Jules Verne's original novel. The book is turned to Chapter One, which is titled "Alarming Rumours!" The actual title to Chapter One in Verne's novel is "A Shifting Reef."
When the giant squid appears, it is swimming toward the Nautilus with its tentacles first. While squid can swim in both directions, they normally move mantle first with tentacles trailing due to much better movement through the water and their gill systems adapted to movement in this direction, particularly if they are trying to swim at a high rate of speed. Also, if the squid was moving with the tentacles in front, they would trail toward the back, not stay rigidly in front of it, like a person's arms stretched out.
When the Nautilus gets back underway after sinking from the New Guinea reef, Nemo states, "There are limits beyond which man and his puny efforts cannot survive, we exceeded them by 5,000 feet." Although not for another 100 years was any undersea craft built for such depth capability, and then only small research submersibles, the conceit of the film is that Nemo invented many advanced technologies far ahead of his time.
The note that Ned Land puts in the bottle, while containing numbers representing both latitude and longitude, neglects to say whether the latitude is North or South. The note is however not useless: the unnamed state could have sent warships to both the North and South locations.
When Nautilus is going through the underwater tunnel, there is some shots from inside the wheelhouse. One can see cliffs passing by directly under the windows. The wheelhouse is situated on top of the submarines hull, so there is no way that the cliffs can be so close to the windows.
When an attacked ship explodes, the men of the Nautilus are thrown AWAY from the explosion. If there was a real explosion, the Nautilus would be blown away from the explosion, and the untethered men would be thrown TOWARDS the explosion.
A split second before the giant kraken clutches the rear of the submarine with its tentacles, the propeller stops rotating. There's no way a mollusk can prevent a ship propeller from rotating without taking severe damage, let alone that quick.
The goof item below may give away important plot points.
A wide shot from above shows the Nautilus entering the flooded crater, with the bow pointing towards the secret base. Capt. Nemo orders all engines stop and makes for the exit. However, in a subsequent outside shot the Nautilus is shown with the bow pointing away from the base.