What an Idiot!/Western Animation/Batman: The Animated Series

Main Series

 * Harley's relationship with the Joker becomes this in-universe. While in her debut she just seems to be a bubbly sidekick, we find out she was a psychiatrist intern at Arkham. The Joker seduced her by promising to tell her all his secrets, and she saw him as a sad sack. After busting him out of Arkham, he hasn't bothered putting on the same persona that she fell for in the first place. Poison Ivy says that he's trash, Janet Van Dorn says that Harley is a classic case of domestic abuse, and Batman outright proves to Harley that he was lying to her about his tragic backstory in "Mad Love" because he's told dozens of sob stories to parole officers and doctors.

You'd Expect: Considering that her fling Poison Ivy says that Joker is bad news, and Ivy never agrees with Batman or the law, that Harley would at least take a step back and try to assess that this relationship is toxic.

Instead: In the few episodes where Harley reviews that Joker is a bad influence and doesn't love her, she snaps back at the slightest bit of kindness from him, whether it's crumbs of praise or a flower and a get-well card after he nearly beat her to death for trying to kill Batman without him.

The Result: Batman Beyond: Return of the Joker happens. When Joker tells Harley he wants to settle down and start a family, which is what she always wanted, she agrees to his plan to kidnap the second Robin Tim Drake, brainwash him into a Joker Jr. after interrogating him for three weeks, and lure the Bat-family into a trap at the decommissioned Arkham Asylum. Harley justifies it as "roughing the kid up" a little while saying she'll make it right. Thanks to her bazooka misfiring, she ends up falling deep into the Arkham foundation despite Batgirl's best efforts to save her. Joker dies that night, courtesy of Tim snapping out of his brainwashing at the right time, but Harley survives thanks to Ivy's chemicals. Offscreen she suffers a Heel Realization about this; as Barbara reveals to Terry, Harley hasn't been seen since or caused any "trouble". It might have to do with the cane she needs to use to walk in the Beyond continuity. Harley starts a new life, settles down with someone who isn't Ivy or a supervillain as far as we know, and has grandkids. She can't ever reveal herself or make amends for what she did because the Bat family would never forgive her for breaking Tim, especially after both Bruce and Batman reached out a few times to save her life, or secure her rehabilitation. Karma then hits her; the DeeDee twins become part of a Jokerz gang, and a resurrected Joker "hires" them to get revenge on Bruce Wayne. The movie ends with Harley agreeing to bail them out of jail and hold her granddaughters in custody before their trial, all the while smacking them on their rear and yelling at them for becoming criminals. They point out that "Nana Harley" doesn't exactly have room to judge them. You'd Expect: Batman to just let this crime go. Hagen was an unwilling villain, blackmailed into crime by a corrupt businessman and unwittingly turned into a monster by the minions of the same businessman. Batman knows of Hagen's past and offered to help Hagen earlier in the same episode. Even if he couldn't justify letting the crime go, nothing stops him from letting him get cured then throw a non superpowered Hagen in jail. Besides, it wouldn't be the first time Bruce Wayne made a public show of supporting the rehabilitation of a criminal, having paid for the experimental surgery and therapies that would restore Harvey Dent to a normal life in "Second Chance". Instead: Batman blows up the machine that is injecting Hagen with the chemicals and says "It's all over, Hagen. The lab boys can take it from here." This leads to an all-out battle which Batman only wins after taking the fight outside where the rain further weakens Hagen. Effectively, Batman murders Clayface by denying him medical treatment... "Batman: Always trying to find a cure, aren't you? Clayface: Can you blame me? Batman: No... but it's made you predictable."
 * In "Mudslide", Batman is chasing down actor Matt Hagen, who has been robbing various chemical factories. Hagen is obviously falling apart at the seams, leaving muddy trails behind him as he struggles to run. Batman offers to help restore Hagen's humanity but Hagen - justifiably skeptical given that Batman nearly killed him in the past - says that he doesn't need Batman's help. It turns out he has found another doctor - a medical consultant from one of his old movies - who has found a chemical process that will restore his body... and the final chemical they need is at Wayne Enterprises, which leads to Batman catching the trail again and finding Hagen's hideout, just as Hagen is undergoing the final process to save his life.
 * Batman does this to Clayface again in the Justice League episode "Secret Society". Granted, Grodd probably wouldn't really have allowed Hagen to be cured of his condition anyway, but still...

You'd Expect: The villains to keep their distance and shoot Batman with their weaponry from afar, perhaps breaking the ice so that he falls in and guard the immediate area so that he can't get back out. This would insure an icy death for the caped crusader. Instead: The villains do indeed submerge Batman after shooting the ice, but not before walking out onto the ice themselves. The predictable happens and Batman comes out from under them, causing the villain's weaponry to go off and break the ice beneath their feet, disarming them and allowing Batman to take them in.
 * In "Cat Scratch Fever", Batman is being chased by a rabid, infected dog through the snowy wilderness with several crooks he was trying to foil also following him. He slides out onto a frozen-over lake and manages to administer a cure to the dog. The villains arrive on the scene, armed and ready against a potentially tired and weakened Batman.

Films
You'd Expect: Bruce to be up front with Andrea and tell her about his struggle and plans and leftover trauma from his parents' death (he trusts her enough to marry her, after all), maybe even think of her as a partner after that surprise sparring match with her. Instead: He assumes he couldn't be Batman because she'd "always be home waiting for me." And this isn't even a universe where female characters have always stayed in the kitchen! Bruce, what gave you that idea that's what marriage had to be like? Well, they both paid the price... You'd Expect: Mr. Beaumont would talk to Bruce and ask to borrow the money from him to pay back what he owes. Wayne is a good guy, and Beaumont can pay him back in a few weeks. Instead: Mr. Beaumont and Andrea flee the country, and Andrea leaves Bruce a note breaking up with him. A few years later, the gangsters track them down and kill him. You'd Expect:Mr. Freeze(wielding a cryogenic energy gun) to have Gregory watch over Nora and go after Barbara himself. This would be a safe way to retrieve her without causing much damage. Instead:Freeze sends Belson(wielding a revolver) to do it for him. Belson, being the impulsive dumbass that he is, ends up starting a fire when his bullets hit some fuel tanks, effectively ruining Mr. Freeze's chances to save his wife.
 * In Batman's Super-Hero Origin story in Mask of the Phantasm, Bruce is struggling with choosing between a life with Andrea and a life as Batman.
 * Also in Mask of the Phantasm, Andrea Beaumont's father embezzled a lot of money from some very nasty gangsters. They've given him 24 hours to give it back, but that's not enough time. His daughter is dating Bruce Wayne, one of the richest men in the world.
 * In Batman and Mr.Freeze: Subzero Freeze and his partner in crime, Dr. Gregory Belson, have just discovered that the vital signs of Freeze's terminally ill wife Nora have stabilized. They take Barbara Gordon, their captive and involuntary organ donor, into the operating room, where Freeze's adopted inuit son, Koonak, sees them nearly kill Barbara to save Nora's life. Horrified, Koonak rushes to stop them, and in the ensuing chaos, Barbara escapes and runs to the outside of the hideout(an abandoned oil refining station.)