Frank Herbert's Dune is a dense sci-fi epic as sprawling as the desert wastes of Arrakis itself, and Denis Villeneuve has done his best to capture its scope with Dune, though his adaptation --and the changes it makes from the source material-- has left some plot holes as large as sandworms running through it.
The movie needed to appeal to longtime fans and new fans alike, so it seemed appropriate for discussions of the Spacing Guild, the High Council, the Imperium, the CHOAM company, and the Landsraad to be removed for brevity. The lack of exposition means that there will always be some things that don't quite make sense, no matter how fans come to the world of Dune.
Where Is The Emperor?
One important figure is missing from the movie, and that's Padishah Emperor Shaddam IV of House Corrino. His pettiness and jealousy over the popularity of the Duke, House Atreides, and its army are the motivating factors for much of the violence in Herbert's novel, but he isn't seen on screen. David Lynch's 1984 adaptation of Herbert's novel makes the Emperor a menace spaced throughout the story.
A throwaway line in Villeneuve's version referencing the Emperor between the Reverend Mother and Baron Harkonnen is hardly enough to emphasize his importance as the Big Bad he's implied to be. Chances are, the whereabouts of the Emperor is a question for Dune: Part 2, but by then fans might not be so convinced of his power and superiority without the groundwork laid in Part I.
Why Isn't The Might Of The Atreides Army Conveyed?
The army of House Atreides is famed throughout the known universe for being trained by Gurney Halleck and Duncan Idaho, its troops matching the Emperor's Sardaukar army in lethality and efficacy. Yet they receive only a few mentions and don't appear to put up much of a fight for the Sardaukar, who are able to overpower Arrakeen.
In Herbert's novel, the reason why the Emperor supplies House Harkonnen with his Sardaukar reinforcements to take back Arrakis is that he's threatened by House Atreides' army and thinks they'll allow the Duke to take control of the Landsraad. The movie could have emphasized the elite nature of the army more assuredly, instead of focusing on what a great swordsmaster Duncan Idaho is.
Why Do The Harkonnens Use Something As Easily Fooled As The Hunter-Seeker?
In order to make an attempt on Paul Atreides' life, a spy left behind by House Harkonnen employs a hunter-seeker to assassinate him in his chambers. This tiny device burrows out of a wall and floats through the air, trying to locate Paul and stab him with its poison-tipped needle, but he's able to outmaneuver it by remaining very still behind a hologram.
The tip of the hunter-seek holds a camera, which continuously transmits a video signal back to the Harkonnen operator. Why couldn't he see Paul? Herbert's book mentions the device's compressed suspensor field as an indicator of its poor vision, but this is never stated in the movie. Why would the Harkonnens, one of the wealthiest houses with the best spice-extracting technology, employ a device that can be so easily outsmarted?
Why Are The Stillsuits Dark In The Desert?
One of the most fundamental parts of life on Arrakis is wearing a Fremen-made stillsuit, which recycles the wearer's sweat and waste into potable water to survive in the desert. In the movie, they're seen to be varying shades of dark gray, with certain Fremen draping theirs in a lighter fabric.
Would someone in the middle of the desert want to be so visible? The coloration helps the actors stand out in the sand to make the narrative more dramatic, but from a more practical standpoint, it would make more sense for them to be a color more closely resembling their environment.
Where Are All The Computers?
Dune is a sci-fi movie set in the far, far distant future, yet there is a notable lack of computers. There are certain machines and large spacecraft, but these are navigated by spice-taking humans who can bend space and time, none of which is made clear in the movie.
In Herbert's book, humankind developed supercomputers long ago that proceeded to try to exterminate them, so after suppressing the uprising of Artificial Intelligence, humankind outlawed any sort of supercomputers from being made. While it's not ideal, a simple piece of exposition outlining this would have gone a far way towards viewers understanding why computers aren't seen and why spice is so vital in their absence.
Why Isn't Paul More Upset That His Father Dies?
After establishing a close father-son bond through some very poignant scenes between Duke Leto I and his son Paul, Leto is killed by House Harkonnen and Paul seems to be indifferent. Lady Jessica has an appropriate paroxysm to confront her grief, but Paul seems to appear cold and detached.
While it's true that Paul might be in total shock, it still seems like he'd have a more visceral reaction at the loss of so important a figure in his life. In Herbert's book, much of his actions are motivated by revenge for the death of his father, so perhaps stronger feelings about the Duke's death will surface in Part 2.
What's Up With Thufir Hawat?
Prior to House Atreides leaving Caladan for Arrakis, the Master of Assassins Thufir Hawat is able to calculate the cost of the trip using incredibly large integers with no trouble at all. This scene is meant to indicate that he's essentially a human-computer who has trained his mind to make computations far beyond a human in the absence of Artificial Intelligence.
In Herbert's book, these human-computers (Piter de Vries of House Harkonnen is also one) are known as mentats, but as the word is never used in the movie, viewers are left confused about the role of someone like Thufir Hawat, who's not only important for House Atreides but is supposed to be one of the more powerful characters in the story.
Why Does Dr. Yueh Betray House Atreides?
Dr. Wellington Yueh is a renowned physician and, bearing the mark of the Imperial Conditioning, a dedicated servant to House Atreides who is beyond trustworthy. Baron Harkonnen is able to make the doctor betray House Atreides, but the reasoning behind his heinous act isn't fully convincing.
Viewers learn that Dr. Yueh conspired to help kill Duke Leto I because the Baron had his wife. However, a crucial scene involving a conversation between him and Lady Jessica about how much his wife means to him, and what House Harkonnen did to her, was stripped from the movie, making his sudden act of betrayal seem like it's coming out of nowhere.
What's The Deal With The Bene Gesserit?
The Bene Gesserit remains steeped in mystery from the moment they arrive in the dead of night to visit House Atreides, leaving fans scratching their heads as to what part they play in the development of the known universe, the importance of Lady Jessica's connection to them, and the importance of Paul Atreides. The Bene Gesserit are a society devoted to not just the development of the expansion of human consciousness, but also to engineering the birth of a specific messianic male figure that will lead the universe to development the like it's never seen.
With the ability to transfer consciousness, they can act as a sort of collective memory for humanity, with beings like the Reverend Mother able to recall dozens of lifetimes. Without knowing any of this, it's hard for viewers to comprehend exactly how frightening the Reverend Mother is, or what her interference means for Paul Atreides, but it's possible their secrets might be being saved for Dune: The Sisterhood or Part 2.
Why Does Paul Act So Non-Chalant Meeting Chani For The First Time?
Paul has several visions of a mysterious Fremen woman in the movie --sometimes to the point of excess-- that are meant to signify her importance in his future. When he finally comes face to face with the desert-dweller after confronting Stilgar, he doesn't act surprised to meet Chani at all.
It would stand to reason that Paul would show more emotion upon finally meeting a woman who's been plaguing his dreams, as well as someone he's meant to be romantically involved with, but the heir of House Atreides couldn't be more apathetic.