In Alien³, Mr. Andrews (the nominal Warden of the prison) is a pretty big Jerkass, but he has very legitimate grounds for not wanting Ripley to walk around the prison freely. He has to keep a population of convicted murderers and rapists in check, who are still very dangerous even if they have found religion. Ripley almost gets raped and perhaps even killed when she wanders off alone. Also, her story about the Alien (which has never been seen on any other planet than LV-426) is admittedly a little hard to believe, when from his perspective the more likely scenario is that Murphy's death was just an accident, and that Golic (who was already an insane multiple-murderer) simply killed the other two inmates.
Animal House: Dean Wormer and the Mayor are, respectively, a jerk and a crook... and their dislike of and desire to be rid of Delta Tau Chi Fraternity are perfectly understandable and reasonable.
The Avengers: Captain America, tired of Stark's egomania, tries to insult his manliness by accusing him of being nothing without his Iron Man armor. Stark effortlessly swats the insult down:
Stark: A genius billionaire playboy philanthropist.
What really makes it this trope, however, is that it's followed by Natasha - not the biggest Tony Stark fan given their interaction in Iron Man 2 - nodding in acknowledgement of the point.
There's also Cap's question to Tony where he asks if he would lie on barbed wire to let others get across safely. Tony's response? Cut the wire.
Batman & Robin has Robin complaining about Batman constantly interfering when the two have a close grip on Mr. Freeze and Poison Ivy during confrontations. Even though most of Robin's actions are out of selfishness and carelessness, he reminds Batman at one point that counting on each other and trusting each other is what being partners is all about. In an ironic twist of this trope, Bruce reminds Robin of this when he tries to get Robin to snap out of Poison Ivy's influence.
The Dude: No, Walter, you're not wrong, you're just an asshole!
In Billy Madison, Eric is a Corrupt Corporate Executive and sleazy Jerkass conspiring to put himself in charge of Madison Hotels. However, he is right when he points out that the company's fifty-thousand employees are not likely to have jobs for very long if the president turns the position over to his drunkard son (who only graduated because his father bribed his teachers). By the end, after some Character Development, Billy himself concludes that he's not cut out to run the business and turns it over to Carl, who is both competent and not a Jerkass.
Brooklyn. Miss Kelly is a self-righteous busybody and a thoroughly unlikeable person. But she's right when she calls out the heroine for seeing a young man from her village, given that she's married to a young man back in New York.
In Calvary, the Dr. Jerk Dr. Harte relishes in telling Father James about a horrible medical incident that happened to a young girl and likens it to the misery felt by victims of sexual abuse who were brushed under the carpet by the Catholic Church. While Harte is clearly just trying to cause Father James pain, he does have a point about the need for justice.
Though not a jerk, Eva Rodriguez is vaguely arrogant (and a rebel, to boot!), particularly early on in Center Stage. At one point, when she calls Sergei on looking at the mirror and uses a certain four-letter word to highlight her irritation at his alleged vanity, the ballet instructor has this to say to both of them:
Instructor: If people want to hear profanity, Miss Rodriguez, they can take a subway. They don't have to spend $60 on a ballet ticket... although she has a point.
Clerks: At the peak of Dante's moaning over how badly his day's gone ("I'm not even supposed to be here today!") and how Randal's the one to blame for it, Randal snaps, noting that (a) he came to work that day of his own volition and (b) most of the bad things that happened were his own fault, such as closing the store multiple times to pursue his own interests, and trying to vainly re-ignite his relationship with an ex by cheating on his current girlfriend. He then criticizes Dante's attitude, noting that he constantly talks down to and belittles otherswhile working a low-wage menial job at a convenience store, and pointing out that although Jay and Silent Bob are stupid, at least they don't try to overcompensate for having what's essentially a monkey's job.
Randal: ...we like to make ourselves seem so much more important than the people that come in here to buy a paper, or, God forbid... cigarettes. We look down on them as if we're so advanced. Well, if we're so fucking advanced, what are we doing working here?
In The Colony, Mason opposes the mission to Colony 5 on the grounds that they're unlikely to be able to help and that the resources would be better spent preserving themselves. He's proven right on both counts. Mason also criticizes Sam for leaving a trail that brings the cannibals back to Colony 7. Sam knew the cannibals were following his footprints and that there was another way across the river, so he knew coming home would directly endanger the colony.
Dirty Harry defends himself early in the movie from killing a guy by claiming he was a rapist. When asked how could he know that he replies "When a naked man is chasing a woman through an alley with a butcher knife and a hard-on, I figure he isn't out collecting for The Red Cross". Mayor admits he has a point.
In Draft Day, Coach Penn often acts like a jerk ass, but he's right when he points out the Browns made a draft analysis and created a playbook with the current quarterback in mind. Months or maybe even years of work has become worthless because of a rash decision by the general manager.
In Deadpool, Deadpool spends most of his time seeking vengeance on Ajax for torturing and disfiguring him.. which he did, but by doing it, Ajax cured his cancer. There is no evidence that his claim - that the torture was necessary to do this - is false, and Ajax even mentions that he was also tortured to develop his own mutations. As for disfiguring him? That's only because he lied to Deadpool that the disfigurement could be cured when it couldn't. Of course, there's also the fact that he normally sells his awakened mutants are sold as slaves, but Deadpool - being an antihero - doesn't seem to prioritize shutting that operation down, even though it would be the right thing to do.
Fatal Attraction With all of Alex's crazed behavior, it's easy to overlook that she's 100% right in that Dan has a legal and moral obligation to the child she's carrying.
Fury (2014): After Norman has had sex with Emma and promised to write her, the apartment she and her aunt are in is caught in the crossfire of a German artillery strike. Norman attempts to reach her body but is roughly dragged away by Grady, who hits him several times and mocks him for a) believing that he would have a fairy tale-style romance with that girl and b) acting like he could still save her. The thing is that Grady, while shockingly heartless, was also absolutely right. Their relationship consisted of an hour or two together, in the middle of a war zone and under very ambiguous conditions. They were unlikely to end up together anyway, and she was now dead. Grady likely saved Norman's life by not letting him try to dig her out.
Walter Peck is entirely justified in his concerns, many of which were shared by Ray and Egon. Weird supernatural occurrences starting exactly at the same time three disgraced scientists start up a supernatural elimination business, using equipment they refuse to talk about, including, by their own admission to each other, unlicensed nuclear accelerators. And when he does originally show up, he's reasonably polite and professional (though one may notice he still addresses Venkman as "Mr." even after looking over his two doctorates hanging on the wall). Only after Venkman takes issue with being questioned by some government stooge and responds with mockery does Peck become unreasonable.
Doctor Yeager, Dean of the Psychology Department sneers down his nose at Venkman, Spengler, and Stanz, make some snarky comments about them, and toss them off of the university's campus, saying, "The thing is Doctor... Venkman. We believe that the purpose of science is to serve mankind. You, however, seem to regard science as some kind of dodge... or hustle. Your theories are the worst kind of popular tripe, your methods are sloppy, and your conclusions are highly questionable! You are a poor scientist, Dr. Venkman!" His criticism is 100% true of Venkman, whose Establishing Character Moment is using an experiment as a means to get laid, causing him to miss an actual breakthrough. Ray and Egon are far more professional, but that just makes their obsession with the paranormal - and their association with Venkman in particular - seem especially questionable. Not the dean's fault that these three weirdos finally found evidence to support their theories less than an hour earlier.
Clamp: That thing that was in here a minute ago, that's dangerous! This guy's from the art department.
Forster: Well, ask him how he knows so much about these "green things".
Clamp: That's a good question Bill – how do you know so much about them?
In Guardians of the Galaxy, Rocket very cruelly and openly mocks at Drax's grief for the death of Drax's family at Ronan's hands. However, Rocket was entirely correct that Drax's loss is nowhere near sufficient justification for almost getting everyone else on Knowhere killed in Drax's attempt to get vengeance on Ronan.
Rocket [mocking Drax]: Oh, boo-hoo-hoo, my wife and child are dead! I don't care if it's mean! Everybody's got dead people! That's no excuse to get everybody else dead along the way!
To his credit, Drax gets the message. Also, while it's not really an excuse Drax was drunk off his ass at the time he did this - he probably would not have thought it an ethical course of action if he were sober.
Ayesha may be arrogant and condescending but her anger towards the Guardians (or specifically Rocket) for stealing her precious batteries, the same things that they were called to guard, is understandable.
Even the loyal Kraglin had to agree with Taserface that Yondu is soft when it comes to Peter.
1960's Home From The Hill focuses on a dysfunctional southern family, the Hunnicutts, in which the mother, Hannah (Eleanor Parker), has hated her husband, Wade (Robert Mitchum) for his womanizing (resulting in one known illegitimate son, played by the A-Team's George Peppard) and has spent the last 18 years making their son, Theron (George Hamilton), dependent upon her. When Wade decides it's time to help Theron "man up" and stop being such a borderline Manchild, Hannah reveals the truth of Wade's infidelities to Theron - which causes him to hate both his parents (Wade for being a jerk and Hannah for not having the strength to do anything about it and both for lying to him). Following some very epic angst for all involved Wade finally seems to realize what a jerk he is and calls Hannah out on playing the victim card for so long and refusing to acknowledging her own Jerkass behavior. After the big reveal he taunts Hannah by saying: "You finally got the revenge you've been waiting for all these years, but what good is it gonna do ya now? He hates me alright, but he hates you too for telling him." He sums it up again rather nicely later on: "We're rotten parents Hannah. This is a rotten home."
Grinch: That's what it's all about, isn't it? That's what it's always been about! Gifts, gifts, giftsgiftsgiftsgiftsgiftsgifts! You wanna know what happens to your gifts? They all come to me. In your garbage. You see what I'm saying? In your GARBAGE! I could hang myself with all the bad Christmas neckties I found at the dump. And the avarice. THE AVARICE NEVER ENDS! "I want golf clubs!" "I want diamonds!" "I want a pony so I can ride it twice, get bored with it and sell it to make glue!" Look, I don't wanna make waves, but this whole Christmas season is stupid! Stupid! STUPID! There is, however, one teeny-tiny Christmas tradition that I find quite... meaningful. Mistletoe. Now pucker up and KISS IT, Whoville!
They did make an attempt to split the money, but couldn't figure out what constituted a fair division since the various parties involved had different numbers of people and only some of those actually went to help the thief and heard about the money in the first place. In fact, Sid Caesar's character went to the trouble of coming up with a pretty complicated formula for dividing it equitably based on all the variables.
In It's a Wonderful Life, Mr. Potter, a Morally Bankrupt Banker, derides George Bailey's late father, saying that he was not a good businessman. It's a point that George concedes, even admitting he has no idea why his father started the building and loan in the first place. However, he then goes on to say that while it wasn't a success by Potter's standards, it helped people move into their own homes.
Jumanji: Welcome to the Jungle: Although she may be obnoxious, Coach Web's arguments to Martha about why she needs to participate in gym class (i.e. "it's physical exercise" and "it's socialization") are perfectly valid.
Claire, before taking a level in kindness, repeatedly talks about the animals as if they are nothing but assets and how important it is to beef up their profit margin and keep the investors happy. Thing is, even if she is a little cold about it, she's 100% right: a park of that size and magnitude would cost tons of money that isn't going to come from nowhere.
Upon being accused of giving Indominus rex unnecessary adaptations to make her a perfect killer, Dr. Wu condescendingly points out that if they ever did use completely accurate DNA, the resulting dinosaurs would look completely different than what the public expects and his explicit instructions were to make dinosaurs people recognized and to make them bigger and scarier to draw crowds. By mixing in genes from so many different animals to produce desired traits, some unintended additions were inevitable. Later subverted when it's revealed that Wu had colluded with Hoskins to turn the I. rex into a living weapon.
Wu also calls out Masrani on the attitude that "We should keep these dinosaurs in their natural environments and not interfere" on the grounds that these aren't their natural habitats- they had to make changes to the DNA to allow these creatures to survive where they are, and virtually nothing on the islands are natural.
Hoskins later points out to Owen, after the Indominus rex has escaped, that calling in what are essentially hired guns to shoot the dinosaurs is the most practical option. Sure, the dinosaurs are only following their instincts, and Owen's raptors have been trained. But not every dinosaur has been trained, the Indominus rex has started killing for sport, and there are more than twenty thousand people trapped on the island until rescue arrives the next morning. Hoskins ends up hitting so many good points that Owen even temporarily works with the hired guns to stop the Indominus rex.
K-9: When Dooley's girlfriend Tracey is kidnapped, the captain points out that it was Dooley's "seat of the pants bullshit" that got Tracey involved in the first place. At the very least, the stunts Dooley pulled to antagonize Lyman at every turn, such as holding him and his guests at gunpoint during a dinner party, didn't help.
In La La Land, Keith tells Sebastian that he's got himself stuck in the past when it comes to traditional jazz, and that it won't do Sebastian any good to achieve his dream of opening a jazz club if no one comes to it. Considering Sebastian's already had to go through quite a Humiliation Conga by that time, Sebastian has no comeback for that. In fact, the next we see of Sebastian, he's joined Keith's group to create a more modern version of jazz.
The Last King of Scotland: Stone, the arrogant Smug Snake British official whom the protagonist hates, turns out to be completely right about Amin's brutality. When Garrigan tries to get help from him, he only decides to if he does his bidding.
If Ben and the rest of the group in Night of the Living Dead (1968) had listened to Harry and hunkered down in the basement, they would have had a much better chance of surviving.
The titular Major Payne is absolutely correct about the effectiveness of his training methods, particularly in how he does succeed to do what no other leader could do by whipping the ROTC Boys into an effective squadron who scores first in the military games. Dr. Walburn does agree, but points out her issue is that this time around they're children so it's morally wrong to treat them with that level of severity and intensity, nor is it necessary for him to be in Drill Sergeant Nasty mode 24/7 (Even his fantasy about an idyllic married life includes a visit from the Vietcong). She ultimately succeeds in getting him to lighten up quite a bit and treat his cadets as children (Though he's still not above shaving them bald for talking back...).
Nixon: Maybe some people would not think of a 19 year old college kid who protests against The Vietnam War as a Jerk Ass, but Nixon certainly does:
Richard M. Nixon: She got it, Bob. 19-year-old college kid.
Larry the Liquidator in Other People's Money. He seems to revel in the fact that he's hated for getting rich by destroying companies. But when people actually talk to him, he's quick to point out that he's just salvaging the value from companies that were essentially dead already.
Kate: You know, you're not very nice.
Larry: Since when do you gotta be nice to be right?
In Pacific Rim, despite his egotism, Chuck Hansen criticized Raleigh and Mako after they inadvertently activated Gipsy Danger's plasma caster and nearly destroyed half of the Shatterdome, not out of malice, but because he was concerned with their ability to do their job and not end up hurting the other pilots.
Raleigh lost his brother and got nearly Gipsy Danger destroyed by refusing orders and engaging Knifehead 10 miles at sea rather than within the golden mile of the coast as ordered - it's easy to see how Chuck can hold Raleigh's rockstar-esque, above the rules attitude in contempt. Then Raleigh starts a physical fight with Chuck and comes close to seriously injuring one of the two surviving Jaeger pilots, which would've left Striker Eureka without a co-pilot and ruined any chance they had of closing the Breach.
By the time Raleigh rejoined the PPDC, almost every other Jaeger and their pilots, except the promoted Stacker Pentecost, has died in combat or from radiation poisoning. From Chuck's point of view, Raleigh never learned from his mistakes, and on top of that, abandoned humanity's only effective line of defense to work on a Wall project that was just proven to be useless. After Raleigh's last Screw This, I'm Outta Here! several years prior, Chuck has no reason to trust that the older pilot will stick around and fight to the very end like all the other pilots have done.
Carolyn is outraged to find out that Johns is a morphine addict when her copilot died in pain without relief. Johns states that the entire reason he's an addict in the first place is because of a piece of a shiv Riddick left right next to his spine that causes him nearly constant pain. He can still feel it rubbing against his spine and shows the wound to Carolyn.
Johns:"You feel that? Riddick did that. He went for the sweet spot and missed."
Johns also repeatedly stresses to Carolyn that Riddick is someone to be genuinely wary of. Johns is a junkie coward and a prick who still operates within the bounds of the law, while Riddick is a dangerous killer who would sacrifice all of them in an instant if he could. Johns's point is proven when Riddick leaves Carolyn, Jack and Imam behind to die when they have outlived their usefulness.
Everything Pete says is absolutely true, since it's all about Ed being The Load and Shaun refusing to grow up. It's telling that Shaun really decides to turn his life around after Pete yells at him to do so.
Deconstructed in Star Trek Into Darkness with Admiral Marcus. He's completely correct in his belief that a war between the Federation and the Klingon Empire is coming, and that it's too late to defuse it so the Federation needs to prepare. However his arrogance causes him to think he can rein in the dangerous and uncontrollable Khan, while his desperation to give the Federation a head-start leads to him committing increasingly amoral acts like trying to kill the Enterprise crew to cover up his crimes. So while the Jerkass has a point, his Jerkassery causes him to both go overboard and botch the job.
SpiderMan 3: Peter may have been under the symbiote's control, but he is right to report Brock for fabricating photos.
Thor: Loki has two very good points. Putting Thor on the throne of Asgard at the beginning of the film would have been a very bad idea. Also, when he accuses Odin of adopting him for political reasons only, it is apparent that it strikes very close to home. The movie does make it clear Thor was a bit of a jerk and acted badly early on and the film is largely about him going through Character Development.
Whiplash: Fletcher's abuse and horrible insults that he spews at his students are all in his effort to push people far beyond their normal capacity and became the best they can be. His methods may be extreme, but as he points out, merely telling someone that they did a good job and then do nothing else can easily squelch the true raw talent hiding inside someone.
In the first film, Senator Kelly defends the need for a Mutant Registration Act by pointing out that there are documented cases of mutants with the ability to walk right through any solid surface, or psychics that can Mind Control people, and ordinary people have no protection against a mutant who would decide to abuse such abilities. In the third film, the President defends his decision to weaponize the "Cure" by saying "I wonder how democracy can survive, when one man can move cities with his mind!" And in the second film, a single mutant nearly assassinates the President despite all the security in the White House. It's telling that despite the movies' villains often being the ones pointing this out, the heroes never have a response to these concerns. Even while there actually are some answers that could possibly be made to these concerns, the heroes never bring them up.
In X-Men: Days of Future Past, Trask justifies the need for his Sentinels to Nixon by pointing out Mystique can shapeshift into any person; she could impersonate Nixon himself, walk into the White House, and order a nuclear attack. Considering all the other things we've seen her do with her powers over the franchise, including the infiltration of the government in such a manner as he warns, his concerns are perfectly valid.
The villains in Logan are unrepentant, amoral, murderous bigots, but they do ultimately have a point regarding Xavier and how dangerous he is. Given that he needs to be constantly drugged to ensure he doesn't turn in to a seizure-induced psychic nuke (one of which nearly kills hundreds of people), an earlier episode of which is heavily implied to have killed off most of the X-Men, and that he actively resists and avoids taking this medication, it's hard to argue against this.
The film Zero Charisma is full of them. The first is after Scott is ousted as Game Master; he angrily states to the others that Miles is not their friend and will abandon them once he's done with his "experiment" i.e. gets bored. Granted Scott is only saying this because of his insecurities, and his inability to cope with not being in charge, but he is right. Miles does eventually abandon them, and returns to his hipper friends excluding the others. Scott even calls him out on this during the party scene.
Miles delivers one to Scott pointing out that, he took nothing from him and it is his own fault no-one likes him.
Nana also delvers one to Scott after he yells at her for welching on her promise to give the house to him. She points out that was in return for him taking care of her, but he doesn't instead she takes care of him. Furthermore, it is her house so he has no claim to it period.
Given the situation, the only logical choice would have been no rescue at all, as Han wanted. They were already in enemy territory with escape being a long shot and they didn't find out she was there until they were already hip deep in trouble.
Admiral Holdo in The Last Jedi is aloof and condescending towards Poe. Dismissing him as just another arrogant hotshot who needs to fall in line and stick to his orders. Given that Leia already demoted Poe after his recklessness got a number of resistance bombers killed earlier in the film she isn't wrong.
Even so, she still has no justification for keeping him (or everyone else, for that matter) in the dark on the most basic outlines of their survival plan while despair is setting in and people are asking for reassurance that the high command isn't just spinning their wheels as time runs out.
Templeton in Charlottte's Web is crass, anti-social and totally obnoxious. But even so, he did a lot for Wilbur and Charlotte and was never thanked properly.
M'Baku, the leader of the Jabari tribe, in Black Panther (2018) is a staunch opposer against Wakandian vibranium and that outsiders may misuse its technology. He is proven correct when Killmonger ascends the throne and wants to use all its technology and weapons to tear apart the world. Also what saves T'Challa's life isn't technology but natural snow and the Heart Herb.
When Shuri, Nakia and Ramonda say that T'Challa was murdered by Killmonger, M'Baku is the one to point out it was through ritual combat that both parties accepted and thus a valid defeat and less murder.