The nature of "Force spirits" has gone all over the place:
In the Original Trilogy, it was assumed that sufficiently powerful Jedi became "one with the Force" when they died, which allowed them to appear as spirits to give Luke advice after death. But in Revenge of the Sith, it was revealed to be a technique that Qui-Gon discovered and taught to Yoda, who then taught it to Obi-Wan. This created a huge contradiction, which raised questions like: Who taught Anakin how to do it? Not Obi-Wan, because he was already in exile when he learned it. Do you still have to be sufficiently powerful, or is it a technique anyone can learn? If the latter, why is Yoda the only one who seems to know how to do it? Why didn't Qui-Gon show up as a spirit to Obi-Wan if he knew the technique (besides the out-of-universe explanation that Liam Neeson had only signed up for the one film)?
A Deleted Scene in Revenge of the Sith tried to fix this by saying it takes a Heroic Sacrifice to become a Force spirit. Okay, that explains Obi-Wan, Anakin, and maybe Qui-Gon. But it doesn't explain Yoda, who quite clearly died of natural causes in Return of the Jedi. Nor does it describe several of the voices Rey hears in The Rise of Skywalker (including Mace Windu, Luminara Unduli, Adi Gallia, and Aayla Secura, who were all killed in regular battle).
The Expanded Universe doesn't know what to do with this. Some works use the Heroic Sacrifice explanation (like what happened to Kanan Jarrus in Star Wars Rebels). Others use the "any sufficiently powerful Jedi can do it" explanation, Star Wars Legends most prominently. And still others use the "technique you can learn" explanation, like Star Wars: The Clone Wars (which makes it a point to show Yoda learning how to do it) — and since that's part of the post-Disney continuity, it's technically the latest canon.
After Senator Palpatine showed up in The Phantom Menace looking like a perfectly ordinary man, many fans were left to wonder how exactly Emperor Palpatine got his distinctive deformed face in Return of the Jedi. Revenge of the Sith eventually explains that his appearance in the original trilogy is the result of injuries that he sustained in a duel with Mace Windu after he deflected his Force Lightning back at him with his lightsaber. But that just raises the question of why Force Lightning never has that effect on anybody else in the series, and why it makes his face all grey and wrinkly instead of just burning him, or how electrical burns could cause him to get features like gnarled fingernails or weird reptilian eyes. It probably would have been simpler to just invoke Evil Makes You Ugly and say that using the Dark Side gradually causes a person to look hideous over time, which is what most people assumed from the beginning.note Alternately, some fans prefer to accept the original explanation from the Star Wars Legends continuity: Palpatine was trying to achieve immortality by using cloning technology and Sith magic to extend his life, and his freakish appearance was the result of his experiments causing his physiology to break down. The powers that be seem to have realized how little sense this explanation makes, as they later said that the change in his appearance was due to a combination of scarring and the force lightning dispelling the Sith Alchemy Palpatine used to alter his appearance, suggesting that he really was Ugly All Along, though probably not quite as hideous as he looks after the lightning incident. If nothing else, Palpatine uses his deformed appearance to manipulate the senate and gain sympathy, so there's some indication Wounded Gazelle Gambit is in play too.
When Jabba the Hutt plans to feed the heroes to the Sarlacc in Return of the Jedi, he claims that its victims are (somehow) kept alive in its belly and slowly digested over the course of a thousand years. In order to explain how a person could survive in the Sarlaac's gut at all (let alone for a thousand years) supplemental materials published as part of the old EU explained that the creature injects nutrients into its prey via feeding tentacles in its stomach, and it slows down their metabolism so that they live as long as possible while trapped in endless agony. While this is certainly horrifying, it poses the obvious problem that the Sarlaac would basically have to feed its own food, meaning that it wouldn't gain any nutrients from eating them (particularly if it took a thousand years just to digest a human-sized creature) and would starve unless it doesn't need to consume nutrients to survive—in which case it shouldn't have to eat at all. A better solution would have been to claim that Jabba was exaggerating, in order to make being eaten alive by the Sarlaac sound more horrifying then it needs to be. Which, considering Jabba the Hutt is a sadist, wouldn't be out of the question. Or that Jabba has no idea what happens to its victims and it's a local myth that he believes.
The Rise of Skywalker attempts to tie up most of the Sequel Trilogy's dangling plot threads by revealing that Palpatine (sensing a pattern on this page yet?) was behind almost everything: he was the founder of the First Order, he created Snoke (who was an artificial human created to do his bidding), and he was responsible for Ben Solo's turn to the Dark Side. But that explanation raises far more questions than it answers. To name a few:
First and foremost: Palpatine was last seen being hurled into a bottomless pit on the Death Star shortly before it exploded—so how the hell is he even alive? The supplemental materials attempt to answer this by explaining that he used the Force to transfer his consciousness into a cloned body maintained by a secret cult called "The Sith Eternal", but that still doesn't explain why he waited 30 years to reveal to his followers that he was still alive. It also raises the question of why the clone looks even older than Palpatine did in Return of the Jedi (beyond the obvious answer of the actor who played him aging), and why the clone looks like a rotting reanimated corpse, and if Palpatine can cheat death by creating a clone of himself whenever he wants, then why does he only have one clone? The novelization of the movie answered this through an interior monologue from Palpatine, explaining that cloning someone as powerful as him was complicated in a way cloning someone like Jango Fett was not, and the clones produced were usually defective and not fully-cloned, with the one he inhabits simply being the closest the Sith Eternal got and still requiring constant medical attention to keep sustained, which explains why he's kept attached to a machine.
Palpatine handwaves his resurrection by claiming "I've died before", which at least sort of an explanation of how he's there, but also raises more questions. Since they never explain why his previous death(s) didn't stick, it's sort of hard to accept that whatever happens in the movie will actually kill him for good this time.
Why did Palpatine put Snoke in charge of the First Order instead of just running it himself? If the First Order is so fanatically obsessed with restoring the Empire, wouldn't they be more likely to follow the resurrected Emperor than Snoke, who was effectively nobody from nowhere? Since the Empire has historically been portrayed as human supremacist (with a policy against allowing aliens to hold positions of authority), it's a bit questionable that they would recognize the alien-looking Snoke as their Supreme Leader.
If Snoke was an artificial being created by Palpatine to do his bidding, then why do Snoke and Palpatine clearly have different agendas? One of Snoke's primary goals in The Last Jedi is clearly to kill Rey, while The Rise of Skywalker claims that Palpatine's primary goal is to possess her. While it's possible Snoke was The Starscream to Palpatine, nothing else in the movies even remotely hints at this. What further complicates this is that at first, Palpatine claimed he did in fact want to kill Rey, and tasked Kylo Ren with bringing her to him because of this, it was only when she came to him on her own that he revealed he wanted to possess her. He only ended up deciding to kill her after all because when she refused to strike him down as part of the ritual and the redeemed Kylo Ren / Ben Solo came to help, he drained their Force dyad and no longer needed her alive.
Most prior Expanded Universe works in the current Canon (including the comic book miniseries Star Wars: Shattered Empire) claim that Palpatine had plans in place to completely destroy the Empire in the event of his death to prevent the Rebel Alliance from seizing any of his resources (called Operation: Cinder). But why would he do that if he was just planning to bring himself back from the dead anyway? Supplementary material was left to provide the answer yet again: bringing himself back to full life and power would take a long time and he didn't want anyone else who wasn't him or his rightful heir Vader (or Luke had he killed Vader and become Palpatine's new heir) taking over the Empire and potentially turning it against him during that time.
Some of the pre-TROSExpanded Universe books outright say that Snoke is his own person and unaffiliated with Palpatine, and even say that he's older than the Empire and watched the fall of the Republic from behind the scenes. Obviously, this can't be the case if he was created by Palpatine at some point between the Original and Sequel Trilogies. Relatedly, some works say Kylo and Snoke are a new faction of Dark Side users distinct from the Sith, which makes no sense if they both work for Palpatine, who is a Sith Lord.
The novelization tries to explain his return by saying that he had set up the cloning facility on Exegol ahead of time, as he had anticipated Anakin killing him, and that he used the Dark Side to transfer his soul into the clone as he fell. This just raises even more problems:
If he knew Anakin was going to kill him, why did he leave him around instead of having him executed?
If he knew it would happen ahead of time, why does he seem so shocked when it happens?
The book says his soul left his body before it even hit the bottom and exploded. So why was he still screaming after his body was supposedly empty?
The Rise of Skywalker also attempts to resolve the mystery of Rey's origins (which had already been explained pretty definitively in The Last Jedi) by revealing that her father was actually Palpatine's son—making her Palpatine's granddaughter. It turns out that her parents actually left her on Jakku to hide her from Palpatine, who was trying to find her to take control of her body. But that just raises numerous questions of its own. Namely:
If Rey's parents left her on Jakku to protect her, then why did they sell her into slavery and leave her in the care of the horribly abusive junk peddler Unkar Plutt? And was a barren desert wasteland really the safest place that they could find to leave their daughter?
If Rey's parents left her on Jakku to hide her from Palpatine while they were on the run from his minions, then why are they buried on Jakku? Did they just...not bother to leave Jakku after they "left" Rey there?
The Rise of Skywalker reveals that Rey's parents were found and murdered by Palpatine's assassin Ochi before they could escape Jakku, which is presumably why they're buried there. But if that's the case, then how could Rey have watched her parents fly away from Jakku in a starship?note After The Last Jedi initially revealed that Rey's parents sold her into slavery for some quick money, most viewers came to the conclusion that Rey's flashback just showed them flying away to a different part of Jakku, but The Rise of Skywalker shoots down that theory. The filmmakers later tried to explain the apparent inconsistency by clarifying that the starship seen in Rey's flashback in The Force Awakens was actually Ochi's ship. Okay...but then why was she yelling "Come back!" at it? Even worse: if Ochi managed to track Rey's family to Jakku, and managed to find and kill Rey's parents, then how did he fail to find Rey? Did he just give up looking for her when he saw that she wasn't with her parents? Later works canonizing Ochi as a Butt-Monkey appear to provide the simplest answer: he may simply be a very incompetent individual who somehow was trusted by Palpatine.
The Last Jedi makes it fairly clear that Rey's parents weren't Force-sensitive, and that Rey developed her Force powers spontaneously rather than inheriting them. But since The Rise of Skywalker retroactively reveals that she actually inherited them from her grandfather Palpatine, that raises the question of why her father (Palpatine's son) didn't inherit any of his powers. And for that matter, how does Palpatine even have a son? Judging by his relative age, Rey's father would have to have been born sometime after the rise of the Empire—when Palpatine didn't exactly have an active love life, for obvious reasons. The supplemental materials attempt to explain this by revealing that Rey's father was actually another clone of Palpatine, and that Palpatine created him as another host body—which just makes it all the more baffling that he didn't have any of Palpatine's powers. It also raises the question of how Palpatine's "son" escaped his clutches long enough to meet Rey's mother and have a daughter with her. And if Palpatine only created his clone as a potential host body for himself, then why didn't he just kill the clone when he found out that he didn't inherit any of his powers? Did he somehow know a child that clone produced would inherit his power, making it another "everything as I have forseen" situation? Finally, if Rey's father was a clone of Palpatine, why does he look completely different? This could have something to do with the "defective" part, but it's never explained.
The book Shadow of the Sith to its credit does try to answer as many of these questions as possible: Rey's parents didn't sell Rey into slavery, they left her with Unkar Plutt on the belief it would be a temporary arrangement while they shook Ochi's tail (having stolen his starship from him in a previous encounter, which is why Rey knows her parents are on the ship and shouts for them to come back despite it being claimed to be Ochi's ship), and that while Plutt was a slimy jerk, they could at least trust him to keep his word until they got back. Unfortunately Ochi captured them in orbit, and being in a very unstable state of mind killed them, before taking his ship to Pasaana, the planet Rey finds his ship, his droid D-O, and his corpse on in Rise of Skywalker, having fallen for a Batman Gambit from Rey's mom of bluffing that Rey wasn't on Jakku, figuring Ochi was too mad and stupid to double-check (and indeed, when Ochi's flunkies tried pointing this out, he killed them). Unkar just took advantage of the fact they didn't come back to his own gain. Kylo Ren's remark about the "pauper's grave" turns out to be an outright lie or at least an incorrect assumption; Luke and Lando found their corpses and gave them a respectful burial, but since they didn't know Rey existed they never went looking for her.
Comic Books
The Force Awakens raises multiple questions about who the "Knights of Ren" are supposed to be, since they're never actually seen in the flesh until The Rise of Skywalker, and we never really learn anything about them other than that Kylo Ren (formerly known as Ben Solo) is their leader. After Luke says in The Last Jedi that Ben "vanished with a handful of my students", most fans assumed that these Jedi students joined Kylo and became the Knights of Ren. However, the 2020 comic book miniseries Star Wars: The Rise of Kylo Ren explains that they're a group of Force-sensitive warriors who are "neither Jedi nor Sith", and Ben Solo became their leader after killing their previous leader Ren (the group's namesake) after he left the Jedi. But that explanation just raises multiple questions of its own. Just to name a few:
Why did Ben take the name of a man he killed? And where did the name "Kylo" come from?
If the Knights of Ren are "neither Jedi nor Sith", then why do they employ a Sith alchemist as their armorer, and why do they seemingly have no qualms with joining Palpatine (the leader of the Sith) after turning on Kylo? For that matter: why is Snoke, a clone created by Palpatine to do his bidding, perfectly all right with his apprentice joining the Knights of Ren and letting them participate in official First Order missions?
According to the comic series, Luke's other students who left the temple actually left to try to hunt Ben down and avenge their fellow students, only to be murdered by him. But if that's the case, how did they survive the massacre in the first place? Why did Luke say that they vanished with Ben? Why would they be stupid enough to try to hunt Ben down by themselves without their master's help? And if they were killed by Ben, why did Luke say that Ben "vanished with a handful of [his] students, and slaughtered the rest" instead of just saying that he slaughtered all of his students?
Literature
A common question about The Phantom Menace is why the heroes were seemingly okay with leaving Shmi Skywalker in slavery. While circumstances may have forced Qui-Gon and Padmé to leave her behind when they initially left Tatooine with Anakin, it's hard to believe that neither the Jedi Order nor the Queen of Naboo would have had the resources to secure her freedom sometime after they left (either by forcing Watto to set her free or simply buying her), making them seem rather callous for abandoning her, even taking into account the Jedi policy of no attachments. Queen's Shadow attempts to address this by showing that Padmé actually did devote considerable time and effort to freeing slaves on Tatooine between the events of The Phantom Menace and Attack of the Clones—but when she tried to free Shmi, she discovered that Cliegg Lars had already freed her. But this doesn't track at all with the events of Attack of the Clones, where Anakin returns to Tatooine for the first time in 10 years to find his mother, and Padmé (who's with him at the time) never says a word about any of this, leaving him to track down Watto to learn Shmi's last known whereabouts, which leads him to Cliegg; if Padmé knew that Shmi was free (and knew who freed her), she could have saved Anakin an awful lot of effort and worry by telling him that.
Video Games
Knights of the Old Republic has swords sharing their melee attack animations with lightsabers, including being able to block them. To patch the question of why the lightsabers don't just chop right through regular swords, it's noted that they're interwoven with the metal cortosis, which is a lightsaber's Kryptonite Factor and can block it. Except every melee weapon-wielding enemy can block lightsabers (and that includes Tusken Raiders using gaffi sticks made of scavenged metal), and lightsabers can't cut through bulkheads or door locks, which implies that cortosis is ludicrously common. But any other source you can find claims cortosis is a very rare metal that is so fragile as to be useless for anything besides countering lightsabers. And if cortosis is so common, it raises the question of why nobody in the game thinks to use cortosis in its more deadly applications, like lightsaber-proof armor or pure cortosis blades that can turn a lightsaber off altogether. A tongue-in-cheek fan theory is that it's only rare because most of it was used up in the KOTOR era when they injected it into everything people could get their hands on.
