Word of God states that in "Ponyville Confidential", the residents of Ponyville shunning of CMC was meant to be justified as "them trying to avoid talking to them because anything they say could end up in print out of context." But they admit that nuance wasn't effectively conveyed in the final product, leading it to be viewed as undeservedly cruel. Plus, the fact that they themselves gossiped about someone before just adds in to the trope and makes the CMC embarrassing them seem more like a long overdue penalty.
Diamond Tiara in "Crusaders of the Lost Mark". According to this episode, her mother is constantly pressuring her to be the best at everything, and to know her place (on top of the heap) and everyone else's (below her). But besides Diamond never showing any regret or conflictedness prior, we've never seen her mother prior and only seen her influenced by her father who was a Nice Guy who reprimanded Diamond's cruelty. Not helping was she was Demoted to Extra afterward despite the writers wanting to do more with her character, giving her no further chance to earn her redemption in the show. She has showed up and done since in the comics, which have been well received.
"The Cutie Re-Mark" was meant to give Starlight a legitimate Freudian Excuse of her childhood friend Sunburst leaving her due to getting his cutie mark causing Starlight to grow up friendless and resentful, then prove herself redeemable by seeking atonement once convinced of the consequences of her wrongdoing. However this was seen as horribly lacking given the severity of her evildoingnote she was a cult leader and kidnapper who stole ponies' Cutie Marks and used frighteningly real brainwashing and even borderline torture tactics on her victims and later nearly doomed Equestria by tampering with time as revenge for said cult's destitution, Starlight seemingly never trying to stay in touch with with Sunburst, and Apple Bloom and Moondancer having gone through similar without villainy. This, along with it seemingly subverting Starlight's higher functioning and well-intentions, caused many to see her as too selfish and irrational to see her abrupt Heel–Face Turn as legitimate, much less earned. That Starlight was unaware of the apocalyptic consequences was undercut as even after being shown she refused to believe it nor showed remorse until Twilight offers an alternative path to making friends made it look like she relented more out of pragmatism than legitimate moral realizationnote Starlight being told how Sunburst's cutie mark lead to all this, allowing Starlight to internalize how her actions caused such harm, only happened after Starlight was displaying her remorse thus wasn't seen as a plausible catalyst for their change of heart (not help by her continued bad decisions in the series afterward). That Starlight was immediately forgiven by everyone, even the town she enslaved, was seen as undeserved given other former villains had to struggle to be similarly accepted despite less serious crimes.
In "The Last Crusade", Shutter Snap and Mane Allgood were supposed to care for their daughter Scootaloo despite being away for so long due to work to the point of missing most of her accomplishments. But since we've never seen Scootaloo with caretakers until this episode, and even they're not there full time (as seen in "Flight to the Finish", where there's no guardian in sight, and as stated in the episode due to their living outside of town) and according to the novel they debuted in only recently started, it seemed they effectively abandoned her. ("Parental Glideance" already confirmed that Scootaloo has confidence issues due to a lack of support at home). Their worry over Sombra's recent attack is undermined by the numerous other times the locals have been endangered over the eight previous seasons, the movie, and semi-canon Expanded Universe works without their apparent concern. This caused many fans, some of whom questioned why they'd have a child if they'd be too busy for them, to think they crossed forgivably flawed to straight neglect.
"Daring Doubt" attempts to give Ahuizotl a redemption story like so many other villains when he reveals that he is a guardian assigned to protect the Tenochtitlan jungle and the historical relics contained therein. He also claims that his supposedly villainous behavior was the result of him being angry over so many artifacts being taken on his watch by Daring Do and Caballeron, and him being in danger of losing his job if that keeps happening. Trouble is, that directly contradicts his previous appearance in "Daring Don't" where he attempted to perform a ritual that would bring 800 years of intense heat, severely damaging the local ecosystem (and worked with Caballeron to obtain the ring he needed for said ritual). If that's his idea of protecting the jungle, maybe he should be fired. And then there are the multiple instances of him sticking Daring Do in some form of Death Trap, in which he had a solid opportunity to explain his situation but apparently decided that Murder Is the Best Solution.
Angel Bunny in "She Talks to Angel". We're supposed to feel bad for Fluttershy neglecting him in favour of her other animals in the episode, unfortunately he crosses the line big time by stealing Fluttershy's body (while this wasn't his fault, the fact he uses his newfound self to torment and bully the other creatures) erases most sympathy we would normally have for him. While Angel did have a point about giving time for all of Fluttershy's creatures and in the series finale "The Last Problem" has apparently passed on, that doesn't change the fact he almost accidentally killed Fluttershy in his old body, when she tried to help.
In "The Ending of the End", Discord was revealed to have impersonated Grogar and brought together the villains for Twilight Sparkle to defeat, to give her the confidence to rule Equestria, unwittingly making them a genuine threat despite his good intentions. After being called out for it and risking his life to redeem himself, his turning Chrysalis, Tirek, and Cozy Glow to stone as a Fate Worse than Death was treated positively, with the villains' actions being portrayed as proof that they were that evil and irredeemable. However, many fans objected as Discord was punishing the villains for crimes that he intended them to commit in the first place, and "Grogar" used violence and Implied Death Threats to force them to partake. What the villains did against Discord's intent wasn't worse than what "Grogar" intended nor their prior evildoingExplanationThey brought apocalyptic scenarios before (Chrysalis indirectly) but wanted to prevent the one they unwittingly caused here as a threat to them. Their attempt to kill the heroes was seen as evil as ever just averting Bond Villain Stupidity.. Nor did Discord give them any chance to redeem themselves, as he himself was given, which was seen as negating the one justification to risk enabling the villains despite the countless safer ways he could have taught Twilight, which is different than what he's called out on.
