Warning: As this trope deals with attempted Heel-Face Turns - more specifically with those meeting resistance and the natural consequences thereof - spoilers naturally abound.
In AI: The Somnium Files - nirvanA Initiative, Lien was a former thief that often worked with the Kumakura family, but eventually left that life behind and went clean. He started working at the Horadori Institute of Genetics as a janitor, but when Chikara found out about his criminal past, he fired Lien, believing nobody who had sank to such depths could ever rise again. Riichi is also extremely distrustful of Lien for roughly the same reason, in one route going as far as hiring a band of mercenaries to try and kill him just so Lien would give up on his daughter, Kizuna.
In City of Heroes, Julianne Thompson had trouble getting heroes to support her ideas for improving the world because of her criminal record charges... that had been manufactured against her by a crooked politician she was trying to expose. Obviously, at some point she snapped, because she eventually became Countess Crey, one of the game's nastiest enemies. You can meet an alternate version of Thompson in Another Dimension where Nemesis has taken over; there, free of her criminal background, she's one of the leaders of La Résistance.
In Deltarune, Susie starts the game as an aggressive bully, but significantly chills out once she embraces her role as a hero and makes her first real friends. However, all of this development happens in the Dark World, so her classmates aren't aware that anything has changed and still treat her as a threat (or, in Noelle's case, a catch).
In Dragon Age: Origins this is a possible fate for the game's first Big Bad, Teyrn Loghain Mac Tir. After being beaten in a duel by the Warden, Loghain surrenders peacefully and seems to express genuine remorse for his past actions. The player is then given the option to either execute him on the spot, or offer him a chance at redemption by allowing him to join the Grey Wardens instead. If allowed to join, Loghain is sincere in his desire to redeem himself and will even be willing to sacrifice his life to kill the Archdemon in the Final Battle. However, for many players (and Alistair, for whom Loghain's betrayal at Ostagar was personal) it was far too little far too late, and many players just cut his head off right there.
Extra Case: My Girlfriend's Secrets: In the ninth ending, Sally turns herself in for the murders "Seira"/Shadow committed, but these crimes go public, resulting in endless harassment that causes her to relapse into Shadow. Marty realizes that even if she serves out her sentence, she'll never be able to return to a normal life, which is why he uses the final time loop to hide all evidence of Sally's crimes.
Final Fantasy IV has the main character Cecil undergo a transformation from a Dark Knight to a Paladin. The regular NPCs in the world don't care, but in the town of Mysidia, which Cecil helped attack in the prologue, several of the townsfolk are bewildered that heof all people managed to become a Paladin◊ and a number of them outright state they don't care if he's a paladin and still hate him.
Final Fantasy VI: When General Celes defects from The Empire, she is met with some suspicion by the members of the Returners. Cyan, whose family was killed by the Empire, immediately mistrusts her. Even Locke, her strongest ally, momentarily doubts her when Kefka attempts to sow discord by falsely claiming she was sent as a Double Agent.
Finding Light: Although Vera wants to atone for her crimes in Mari and the Black Tower, the forest spirits refuse to forgive her, preventing her from spawning new nymphs.
Radiant Dawn has a non-villainous example in Rolf's mother, who abandoned him, Boyd and Oscar at a young age after their father became fatally ill. When she shows up in the game claiming to have regret leaving the brothers alone with their dying father and begging to have her son live with her again, Rolf decides he does not need her in his life and refuses to see her.
Awakening gives us a rare male Broken Bird in the form of King Gangrel... yes, that Gangrel. Should you recruit him in his Spotpass chapter, the player will discover, via supports and quotes, that he regrets all of the actions that he did for the first part of the game on an incredibly deep level, and he has absolutely nothing left to fight for. The Avatar cuts him a break (moreso if a female Avatar marries him), and he even looks out for Emmeryn, the same woman he wanted dead, if she joins your group. Despite most of his actions being unjustifiable, Chrom is never able to forgive him. And Gangrel is painfully aware of how this is a consequence of his own actions — even when he had a bit of a Freudian Excuse of his mother dying, this is not enough of a reason for him to do the horrible things he did. (Walhart and Aversa, the other Atoners of the game, at least did the just-as-bad things they did after being brainwashed/manipulated by the Grimleal, unlike Gangrel who did them out of his own will.)
In Galaxy Angel II, the Valfask race get this treatment. After the events of the original Galaxy Angel trilogy, many of them joined the EDEN military in an effort to integrate peacefully, but many EDEN natives still remember the atrocities they committed in their bid for conquest across the universe. The Luxiole's new chief operator, Tapio Ca, does not resent this attitude, and he admits his race's previous actions were evil and the wariness towards them isn't unjustified.
Injustice 2 has Hal Jordan (Green Lantern) and Barry Allen (The Flash) have a Heel–Face Turn from the previous game where they willingly surrendered after realizing that serving in Superman's regime wasn't a good idea after all. Both men deal with the hardship of themselves trying to reform while the citizens don't trust them. Barry does his best to keep going despite the distrust while Hal is tired of everyone not giving him a second chance despite how much hell he had to go through to become a Green Lantern again. Barry convinces him to keep fighting for what's right no matter what, which eventually gets Batman to start trusting Hal again. Harley Quinn, who used to be the bad girl for the Joker, also deals with similar problems after joining Batman, but she doesn't let it bother her.
In The Legend of Spyro, even though she had been Brainwashed and Crazy under Malefor's control, there are still many characters who still distrust Cynder post-reformation, despite her and Spyro doing their best to save the world.
LISA has Marty, Brad and Lisa's abusiverapist father. He's a complete and utter Hate Sink, and he's the reason why Lisa is dead and Brad is so screwed up. But when Brad meets him again on his search for Buddy, Marty is a completely different person, protecting Buddy with no ulterior motives and coming to her defense when Brad attempts to take her against her wishes. Brad understandably cannot forgive Marty for the things he did and beats him to death in front of Buddy.
Subverted with Elnora, a young Asari Eclipse initiate on Illium. When Shepard and co. plow through an Eclipse base to recruit Samara, "little baby Anora" puts on a façade of being an air-headed repenter begging Shepard to let her go. A journal the team finds in the next room, though, show it was an act hiding disturbing sociopathy in her murdering a volus merchant, leading to Samara's investigation.
Most villainous characters... Saren, or the Illusive Man, or even Harbinger or Morinth are people Shepard can at least be civil to. Not so with Gavin Archer, the former director of Project Overlord in ME2. Finishing the "Overlord" DLC reveals Gavin used his autistic brother, David, as a tortured lab rat to decode geth transmissions. Shepard shows utter disgust at Gavin regardless of alignment. Come the rescue of Cerberus defectors on Arrae in ME3, Shepard treats him like utter shit regardless of how contrite he is over torturing David.
Mewgenics: The song "Mom I Really Hate You", the radio version of the boss song "Ice Age Unga Bunga" changes the caveman-sounding gibberish to a song about a mother begging to be part of her child's life again, only for the latter to reject it because of how much she made them suffer in the past.
Murdered: Soul Suspect: The protagonist Ronan O'Connor is a Reformed Criminal who became a member of the Salem Police Department; regardless, his fellow officer, Baxter, adamantly refused to see him as anything but another crook.
Perseverance: Full Clearance: Downplayed in regards to Esperia, who wiped out Britain and killed Pep's mother in front of him. Nola doesn’t completely forgive her for her crimes, but is still willing to work with her to restore Pep’s mortal psyche.
Blue Umbrella in Resident Evil 7 aims to clean up the mess that the now defunct Umbrella corporation had made through out the series. Chris Redfield, who had dealt with Umbrella's plans many times in the past, does not trust Blue Umbrella even as they work together.
In Romancing SaGa: Minstrel Song, one of the short stories Broken Bird Schiele tells your hero takes a particularly cruel twist on this: A reformed pirate raises several children he had orphaned, only to have them take out their revenge after reaching adulthood.
The aversion of this trope is notable in the Sith Warrior story in Star Wars: The Old Republic. After the betrayal of Malavai Quinn (in the beta you could kill him as a result but in the final game you can't kill your companions) there isn't even a hint in the conversations that the player character might not trust him because of those events, which would actually be very understandable.
In Stellaris, the Cybrex were a synthetic species which waged a war of extermination against all organic life accompanied by atrocities such as experimenting on captives. The Cybrex eventually realized their actions were wrong and retreated to a ring world in an isolated system, avoiding all contact with the rest of the galaxy. Their former enemies eventually located the ring world and destroyed it along with the Cybrex who chose to not resist.
In Super Robot Wars 30, Char Aznable goes through this when he shows up due to his attempt to drop Axis and, to Kamille, Koji and the Getter Team, feel that it's a slap in the face due to the fact they thought he and Amuro were dead (they weren't). Lelouche suffers this as well due to his actions as emperor before his own temporary death and resurrection.
A non-villain example in Luke fon Fabre from Tales of the Abyss. Luke begins the game as a selfish, bratty, extremely naive ManchildJerk with a Heart of Gold due to his sheltered and spoiled upbringing since his kidnapping and gaining "amnesia". After his My God, What Have I Done? moment where he is forced into destroying a whole town by the Big Bad, he spends the rest of the game trying to convince the entire world that he's changed his ways. The above quote comes after Jade shows that he clearly doesn't trust Luke after meeting up with him, and Anise has a similar reaction when meeting with Luke again. Considering Luke has been recently revealed to be actually seven as he's the replica of the original Luke and he was set up to fail from the start, this treatment can come across as extremely harsh to the audience.
In Trauma Team, Maria loudly and violently rejects CR-S01's genuine attempts to make amends for the crime he might have committed, driving him into a Heroic BSoD which he has to be talked out of by the agent who captured him. After this, he does manage to convince Maria of his good intentions, but the initial rejection was pretty harsh.
Valkyria Chronicles II has Sigrid Essel, a former member of the rebels join Class G after Reiner's event. As expected, no one in the academy is warm to his defection from the rebels, and his classmates question Avan's judgement in allowing him to join with them. He's even accused of being a spy for the rebels, which he has to endure day in and day out.
This happens for a short time in if you play a Death Knight. After the prologue area, you are teleported to Stormwind or Ogrimmar, and face lynch mobs demanding your death. Thankfully, speaking with Thrall or Varian provides enough reputation so this isn't too much of an issue for death knight players.
Later, in Borean Tundra, Thassarian is sent on a Suicide Mission by General Arlos (who is later revealed to have been brainwashed by a Scourge agent).
The Forsaken are undead who managed to break free from the Lich King's control through sheer willpower and simply want the right to exist. The fact that their own brothers and sisters want them destroyed has only made them more bitter toward the living.
This is also half the reason for the game's overall storyline; the Alliance understandably has a hard time accepting that the new Horde is ideologically opposed to the one that razed their cities to the ground. The fact that they're still a war-like people who raze their cities to the ground doesn't help.
Sylvanas Windrunner made a lot of enemies over the years, especially with her atrocities during the Fourth War in service of the Jailer, but she eventually turned on him and aided in his defeat. Despite seeming to genuinely reform, many of her victims she despise Sylvanas and she was sentenced to a possibly eternal penance saving souls from the Maw, many of whom reject salvation specifically because it comes from Sylvanas.
◊ and a number of them outright state they don't care if he's a paladin and still hate him.