Plot hole: At the end of the movie, as Morbius lay dying, he had Commander Adams press a lever that irreversibly set the countdown for the planet's destruction. Morbius said earlier in the movie that they were in a learning laboratory for the Krell children. Why would the Krell have given their children access to something so dangerous to begin with, in a place where the switch didn't belong, and without any safety precautions to prevent an accidental countdown?
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: Morbius says no physical representation of the Krell remains. Yet later he shows the Commander a screen that contains the total sum of the Krell's scientific knowledge. So didn't the Krell study their own biology?