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 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.
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.