Plot hole: Krell doorways and equipment suggest they are short, wide and 2-3 times larger than a human. Yet the shuttle pod the Commander, Doctor and Morbius ride in is designed for human size beings.
Plot hole: When Fogg convinces the cargo ship captain to take him to Shanghai, he pays for the passage of himself and two of his colleagues. One of these colleagues is Aouda, but as Passpartout is not there, the other one must be Fix. Why, then, does Fix have to pay for his own passage? If you notice, Fogg seems surprised to see Fix on board.
Suggested correction: At no point do they travel to Shanghai. They travel from India to Hong Kong to Yokohama. There is no scene where he negotiates with the cargo ship Captain. And he is definitely not surprised to see Fix. Are you sure you were watching the 1956 version?
Suggested correction: Just in case Passpartout does show up at the last minute? Also, knowing Phineas Fogg, he has probably already hired Passpartout's replacement and it is for him.
Plot hole: After being denied permission to contact the aliens by himself, Dr. Marvin returns to his hotel and calls them up on the radio anyway and arranges to meet, despite not being allowed to leave the hotel. His wife says she overheard him say he's under orders not to leave and begs him to call someone instead: "Call Huglin". She shouldn't know who Huglin is because Huglin was only assigned to guard them as Marvin was being denied permission to contact the aliens.
Plot hole: When Becky falls asleep she is awakened by Miles and has now become an alien, However she should have died and her essence should have been in one of the pods. There were none nearby.