In Batman: The Killing Joke, the first half has Batgirl constantly whining about how Batman "doesn't take her seriously," ignoring the fact that every time she tries taking on Paris Franz, she nearly gets killed in the process while Batman rescues her. His concerns, thus, are perfectly valid.
In Mulan II, Shang is meant to be a cold-hearted jerk for opposing the princesses' affection for the soldiers, but consider that their country and the other kingdom is at stake, and the arranged marriage could save them from the invaders. Basically, Shang is in the right when telling off Mulan for being glad that the princess have fallen for Yao, Ling, and Chien Po, but no one really mentions that.
In Showgirls the main character Nomi works in a strip club and aspires to be a topless dancer in a Las Vegas show. At one point she gives a man a lapdance that amounts to sex with a denim condom, she was perfectly willing to do what came down to live, on-stage lesbian sex, screwing her boss to get a higher position, and pushing the lead dancer down the stairs to get her job, but when she's asked during an audition to use ice cubes to make herself more *ahem* "perky", her angry refusal is treated as a display of strength of character. Why the line of moral compromise is drawn at that exact point is perhaps the only thing the movie leaves to the viewer's imagination. Furthermore, her later use of ice cubes after she joins Goddess is intended to be a sign that she's "losing herself."
In Surrogates - and, for that matter, almost every movie about virtual reality - it's taken as a given that using artificial means to lead exactly the kind of life you want is inherently morally inferior to actually going out and leading your own boring life. Even though the users feel and experience everything their surrogates do (so it feels just as real as doing it in person except you won't die if, say, your parachute doesn't open), and actually are interacting with other people (they just don't see what they really look like), and the movie tells us in the opening that the use of Surrogates has almost completely wiped out racism and sexism. Not only that, but they had no murders for over a decade in the city of the film. Yeah, but ... it's not real, man! To really hammer home the informed wrongness, Spicy City has an episode called "Love is a Download" with an almost identical concept to Surrogates, except it is shown as a happy ending when the two main characters, a victim of domestic abuse driven to suicide from always being treated as a sex object due to her looks and a hideously ugly computer technician who's been alone his whole life because of his looks, find love within the virtual world where looks don't matter.
Similarly, in The Matrix. Cypher is the only one to see Matrix life as preferable. Granted, he killed almost all of his allies and also handed over Morpheus so that the machines could get the codes to Zion to finish off the rest of the free humans, all for a chance to return to the Matrix (with the possibility of him being Rewarded as a Traitor Deserves), but still. The Matrix is treated as a horrible prison, and the machines as monsters for treating humanity that way. When in fact, the people who live in the Matrix are living better lives and people in the real world struggle just to survive. The real world planet has been turned into a total wasteland that can barely support life. Also, in order to get recruits, Morpheus deceives them by sparking their curiosity through extremely vague descriptions, no mention of a war that they are now obligated to be a part of, and also no mention of the fact that life in the real world completely sucks. Yet freedom is treated as the ultimate goal because, um, it's real or something. Cypher puts it best when he says "If you'd [Morpheus] told us the truth, we would've told you to shove that red pill right up your ass!" Made worse when it's mentioned that the Matrix originally was a perfect paradise for people, but human minds just wouldn't accept a perfect world, so the less perfect current version of the Matrix is essentially as good as they could do. The movie never actually says his points are wrong, except for the part where he's willing to kill people in cold blood to achieve them, and to give up Morpheus. And the first part isn't that different from how Zionites treat people in the Matrix.
Ed Rooney in Ferris Bueller's Day Off is depicted as a JerkassDean Bitterman who's going overboard with trying to discipline Ferris (admittedly, he broke the law and committed animal cruelty), though that doesn't change the fact that Ferris is skipping school, has done so at least nine times prior (he hacks into the school computer to change the records), and does so by blatantly exploiting the good will of everyone, including his parents.
A movie called Women Obsessed shows a man physically beating his new wife and menacing his stepson. At one point he seemingly rapes the wife (which is a case of What Happened to the Mouse? since we don't see what happens after he closes the door). She gets pregnant by him and ends up losing the baby. He carries her six miles to the hospital. At the doctor's house, she tells the doctor that she wants to leave him because he's abusive. The doctor then chastises her because of his heroics last night. She's portrayed as wrong in this situation and the movie ends with her begging him for forgiveness. This is also a case of Values Dissonance, since the movie was made in 1959, a time when attitudes towards spousal and parental abuse were in several ways very different.
Mickey in Shes The One falls out with his new wife Hope for assuming he would go to Paris with her without discussing it with him first, which seems like a reasonable point, yet he is blamed for it and says himself that he ruined the relationship. The only reason given for him being to blame is that he "didn't fight for her" but Hope didn't fight for him either and was in the wrong in the first place.
School of Rock depicts Ned's girlfriend Patty as being pushy and hypocritical because she "forces" him to demand Dewey actually get a job and pay his massive rent debt. Even though this is a rather reasonable demand, since Dewey isn't terribly concerned with what a drag he is on Ned. She is also supposed to be seen as hypocritical by pointing out that Dewey steps all over him and manipulates him...even though he does exactly that to Ned. To the point of engaging in identity theft to get a job under his name and trying to beg that he not do anything about it when Ned finds out. She's later further villainized for convincing Ned to press charges over the identity theft. At no point in the film is Dewey ever truly sorry for what he pulls on Ned and how many laws he broke or even that what he did could seriously impact Ned's own career as a teacher. For starters, the income from the job that Ned technically lost out on since Dewey took it from him, or what would happen when Ned didn't declare income from a job unknowingly taken under his name on his taxes. Dewey does acknowledge that what he did to the kids was wrong, but he's not ever aware of how much he took advantage of his roommate either. The moment where Ned breaks up with Patty for Dewey's concert is supposed to be a triumph of assertiveness when her only crime is being kind of aggressive over Ned not ever standing up for himself and being taken advantage of. Along that line, the parents of the children in Dewey's class aren't exactly unreasonable for being upset that their kids are learning nothing but rock music, and no academics, for weeks or months on end. Even many rock-loving parents would be bothered by how this would set their kids up for some serious educational problems later in the area (for being behind all the other classes in their grade).
In High School Musical, one of several mean things Sharpay does...is help the shy new girl at her school become friends with people who genuinely like and support her. Something Gabriella - the girl in question - openly appreciates. Admittedly, Sharpay only did that because she wanted to distract Gabriella from Troy, but it's still hard to take it as a malevolent act.
In The Avengers (2012), the titular group gives Nick Fury hell and a half for SHIELD using the Tesseract and recovered HYDRA technology to make weapons of their own, which Fury justifies because humanity is hopelessly outmatched by the likes of Asgardians and otherworldly threats. Nothing is said of the simple fact that Fury is absolutely right, especially considering humanity's only other hope, the titular Avengers, are currently a ragtag unreliable group at best and that if they fail to come together or are otherwise defeated humanity will be completely helpless. The criticisms also ring very hollow coming from Iron Man and Captain America, the former who relies on making weapons like SHIELD is doing and the latter who was created by the predecessors of SHIELD through a scientist rescued from HYDRA.
In Ant-Man, the villainous Darren Cross, determined to uncover the secret to shrinking technology, orders animal testing on lambs. His aide Hope is horrified (since the failed shrinking tech dissolves them into a tiny puddle of bloody goo) and asks why they aren't testing on mice instead. Cross snarls that there's no difference, but despite his ruthlessness he does have a point: both are just laboratory animals, and a mouse is too small to test shrinking tech that would eventually be used on a human. Also, the fact that Hope objects to the use of lambs but not mice indicates that she's more motivated by the lambs' cuteness rather than actual ethics.
In Spider-Man: Homecoming, the mentor-pupil conflict between Tony and Peter is supposed to be seen as Tony being the Experienced Protagonist who is right and correct, and Peter is the eager student getting too big for his boots. The problem with this is that Tony's "mentoring" of Peter just consists of him having Peter run around with the Spider-suit without teaching him how to use it and with no supervision other than Peter leaving Happy Hogan voicemails detailing his daily activities. At no point does Tony clarify why exactly he is training Peter in the first place, or what he expects of him, or how the latter fits in with his long-term Story Arc (post-Avengers 1) of preparing Earth for another alien invasion. Additionally, many of the things Tony chastises Peter for doing (being reckless and causing collateral damage) are things that Tony himself is guilty of and on a larger scale, making him come across as a complete Hypocrite. Lastly, when Peter tells him about the Vulture and his alien tech, Tony dismisses it as below the Avengers' pay grade and tries having a bunch of FBI agents take care of it, without telling Peter his plan, with disastrous results. The end result is that Tony comes off as a poor mentor who unfairly berates Peter for his own screw-ups.
Han Solo is repeatedly portrayed as being in the wrong for wanting to leave to pay off his debt to Jabba the Hutt in The Empire Strikes Back. Nobody (except General Riekann) acknowledges that he is a dead man if he doesn't pay it back, or that he's actively being hunted by bounty hunters who have already attempted to kill him in Mos Eisley and on Ord Mantell by the time the second film has started. Even when Han points out his concerns that the bounty hunters won't stop hunting him until he pays off his debt he's nevertheless dismissed as if he's just turning his back on the Rebellion's cause, and the possibility of leaving, paying his debt, and coming back is never brought up either even though this would probably take only a day at most.
In Home Alone, Kevin is portrayed as wrong for being afraid of Old Man Marley, with even the man himself politely chastising the kid for not being more friendly. Thing is Marley seems to go out of his way to be unnecessarily creepy at every opportunity, towering over the kid and glaring in a frightening and even threatening manner without speaking whenever they run into each other outside, making it pretty damned hard to fault the kid for being afraid of the guy even if he hadn't been fed a false "the guy's a murderer" story from his brother. Your totally average adult would be threatened by this kind of behavior. Not to mention, Kevin actually does warm up to the guy the second he drops this behavior and acts normally in the church, which passes without mention, making it pretty clear the kid wouldn't have been afraid of him if he didn't act the way he normally does.