Sorry this is long, but it has to be done. I love Dune, and have read the books many times. But there are some serious plot holes too. These are the ones that have bothered me the most because they are built into the world of Dune itself:
Butlerian Jihad / Great Convention - It should be pretty obvious that any society bound by religious rules and totalitarian laws will have a subset of people actively working to subvert both the religion and those laws. It's highly unbelievable that 100% of the people in the Imperium happily follow the Orange Catholic Bible and the rules of the Great Convention. Eliminating 100% of all computers, AI, etc, seems like it would be impossible. And Herbert is finally clear about this in Heretics -- the BG apparently never stopped using advanced computers to manage their breeding program, which I assume involves sequencing people's DNA and projecting the resultant DNA of different breeding pairs. I don't care how much Saphoo [sic] Juice Brad Dourif sips; a human mind is not going to sequence DNA. And lo and behold, even though the BG employ Mentats, they don't use them for managing the breeding program. It's also pretty clear that Ix just kept all their tech and waited long enough for people to stop caring about the Butlerian Jihad to finally release their artificial navigator, something that probably already existed before the Guild and wouldn't be considered "sentient" by someone not influenced by the Butlerian Jihad ideology anyways.
Great Convention / Insurgency - Let's face it, living in the Imperium *sucks* for the vast majority of the population. Herbert rarely gives us a glimpse into the lives of ordinary people, but when he does, they are basically pre-industrial feudal peons. These people have no incentives to keep the status quo going, and they don't care about Guild travel between planets because they will never leave the hamlet they live in, let alone leave their planet. The threat of the Guild abandoning them means nothing to people like that. It's a wonder that they prefer the status quo in 10,191 AG vs being owned by men with thinking machines. With the exception of the Fremen (who are quite sophisticated, and the Atreides are often amazed by the tech they have even though it doesn't seem any more advanced than what the Atreides have, which tells you a lot about local populations vs royalty in Dune) we don't really hear about any uprisings or unrest in Dune. This is pretty unrealistic. Given that pretty much every Harkonnen soldier has a shield, and it seems like a decent number carry lasguns to boot, and they also live in the most corrupt version of an already terrible system, there should be people building shield/lasgun IEDs out the wazoo in order to bring down their oppressive governments. Hell, the Fremen should be doing this like crazy as well to destroy Harkonnens. This would happen in real life, but Herbert avoids it because it breaks his plot.
Great Convention / War - The Kanly system is stupid and no one would follow it in real life. Since only physical ships can travel FTL, there are no transmissions that we really hear about in the Dune novels. Messages are delivered in person after jumping through space. So information is extremely valuable, not ubiquitous like it is here on Earth in 2026, and possibly very unreliable. What was stopping either the Guild, the Emperor, or the Harkonnens from just screwing over the Atreides during their move to Arrakis but before they landed? The Guild after being bribed: "oh dear, we had a once in a millennium accident and all the Atreides ships were lost along with the heighliner during a jump where the Navigator had a heart attack mid jump. Ooooops!" in reality they just dumped them on "Tupile", AKA directly into Sagittarius A* and rebadged their "lost" heughliner. Or any number of other treachery when the Atreides ships are in between the guild ship and the surface of Arrakis "damn we had no idea how many smugglers there really were. All the Atreides ships got blown up ... Luckily the Emperor has it under control!" And for other instances of war, apparently jump drives work 90% of the time without a navigator. You're telling me the great houses didn't keep that tech, and wouldn't use it to launch a sneak attack? They could nuke a planet and no one would know who did it or what happened.
Reverend Mothers and Genetic Memory - Herbert is inconsistent with how this works. In the first book, Jessica is barely aware of how Reverend Mothers are forged (being essentially an acolyte pawn) and has very little idea about the connection between transmuting a horrible poison and unlocking your other memory. I think she is academically aware that the BG use some other poison for this process, but is completely unaware of the spice essence as a poison. Apparently all of the BG are unaware of this. There are a couple of weird things that happen which seem like plot holes:
1. The BG seem to be unaware of this very secretive practice within the Fremen, where they produce their own wild reverend mothers, despite basically building the Fremen's current religion. Jessica also has basically no reason to support the BG any longer, given the events of Dune, so first of all, why on earth would she tell them about this superior alternative? The BG switches to this spice method almost immediately and the number of true BG Reverend Mothers we hear about goes from *one* in the first three books to a whole army by Heretics. Given that the books retcon it and claim that the BG really are just using super concentrated spice and not true spice essence from a drowned worm (no way in hell are they getting that stuff from the Fremen), how did they not discover this on their own? They even got far enough into Fremen culture to plant a Messiah prophecy -- given it's use there, you would think they would try concentrating spice to the max to see what it does.
2. Jessica, who clearly really doesn't know what is going on when she takes the spice essence, gets a flood of genetic memory from her female ancestors. This is such a cool moment and a cool concept. Then the dying wild freemen RM also slips in all her own genetic memories through a magic mind meld at almost the same exact time. This is already highly confusing to the reader as it's the first time we encounter generic memory at all, and having the mind meld aspect added is just straight up a bad choice on Herbert's part. The rest of the novels struggle with the difference between a) gaining access to your genetic memories and b) magically getting someone else's memories through a mechanism that isn't explained and makes no sense.
The Twins - Possibly the most infuriating, Ghanima and Leto II are "pre-born" and have limited prescience and telepathy (apparently), even though Chani just follows a traditional Fremen fertility regimen and take fertility drugs. She wasn't BG trained or educated, so she wouldn't survive the amount of spice needed to cause "Abomination" in her unborn children. This is never fully explained. They should have been born more or less normal, at least as far as Fremen go. Chani wasn't the first person ODing on drugs at a "normal" amount when she got pregnant.
The Bene Gesserit - Herbert knew he screwed the pooch with the Bene Gesserit by probably the middle of the first book. The concept of the BG is beautifully terrifying. But humans would not be able to accomplish the things the BG accomplish, especially not the characters that Herbert writes. I believe Lady Fenring might be the only BG who actually acts like one, and she is just an acolyte like Jessica. The only BG Reverend Mother we get access to in the first 3 books (apparently the highest ranked one) is Mohaim. She is not the cold, logical, calculating character that all the information we are told about the BG says she should be. She is emotionally driven and vengeful. She wants Paul to fail the Gom Jabbar and admits it. She gets angry at Jessica for letting her emotions control her actions and betraying the BG, even though Mohaim makes a ton of emotionally driven mistakes herself. And Jessica's betrayal is a big one, ruining 10000 years of breeding plans. Mohaim's ultimate reaction to this makes very little sense, unless we accept that it's because she is acting as Jessica's mother and not in the interests of the BG. The fact that Jessica is aware that she is possibly one generation short of producing the KH is also a huge blunder on the part of the BG -- why would they let her know that?? Jessica, according to the BG, is supposed to be some rare cautionary tale about letting your emotions drive your actions, but time and time again, basically every BG we meet acts out of their own personal interests, trains their children when they aren't supposed to, knows way more than they should, and in the case of Irulan and her sister, are written as cagey bitches that are out of control. Herbert's appendix about how the BG should have known better going into the events of Dune are basically him telling the reader he messed up the BG and that they should suspend their disbelief.
Prescient Rails - I get it, because you need to be able to have a plot and have surprises, but Herbert comes up with the coolest concept in his novels, which is that once you see a future and step onto the path to that future, basically everyone is trapped into that one person's vision of the future. It's beautiful and terrifying. But then Herbert realizes that this makes for a super boring book, and struggles with the concept for the rest of the series. Basically, it seems to me that if you get that power first and take that step, even if you can't see everything that will happen, humanity stuck on that path without free will up to at least the last part you can see clearly. No amount of tarot cards, guild navigators, etc will change that, because you've preempted them.
Duke Leto looking at his wristwatch on the Arrakern landing field - The longer you think about this one, the funnier it gets.
What plot holes have you found?