There are some seriously dysfunctional anime families out there, and the fault usually lies with the horrible anime parents. Shockingly, not all of them are the terrible parents from Yu-Gi-Oh!. In fact, you'll find bad parenting in anime of all kinds, from Elfen Lied to Pokémon.
Whether they're forcing their kids to commit suicide for insurance money or transforming them against their will into man-eating monsters, bad parenting in anime is rampant. In fact, it's probably more common than good parenting. Let's learn about the worst parents in anime, and pray that their barbarous parenting techniques never transfer over to the real world.
Shou Tucker is, far and away, one of the worst parents in fictional history. What makes him so awful? Well, in order to maintain his position as a state alchemist, Tucker uses alchemy to merge his daughter Nina with their pet dog. Let that sink in. Now go take a nine showers, and lament the fact that you still feel gross.
He briefly passes off the monstrosity as an "ethically" created chimera capable of speech, but it's quickly discovered he couldn't possibly have done this morally. While he's waiting to be arrested for his crimes against both human and animals, he tries to solicit sympathy from his mutated child by telling her he's misunderstood. Not much to understand, dude, you're willing to destroy your own child and your beloved family pet for a job.
Mayu, one of the most innocent characters in Elfen Lied, ran away from home at age 14 to escape her horrible parents. That alone should tip you off that things are pretty bad. Mayu's stepfather is a sick man who takes advantage of his new stepdaughter almost as soon as he meets her. When Mayu appeals to her mother for help, her mother slaps her in the face, calls her a liar, and tells her that she is unloved and unwanted.
This lady cares a lot more about her marriage than she does about her daughter's well-being, and she is more than happy to continue a relationship with a pedophile. When Mayu's stepfather violates her again, she leaves home, unable to take the abuse anymore.
In general, it's not a great parenting move to try and force your kid to conform to a gender identity they don't agree with. Hiromi Shiota wanted a daughter so she could vicariously relive her own girlhood (which was admittedly terrible). When she gave birth to a son instead, she decided it didn't matter and raised Nagisa as a girl. Much to Nagisa's chagrin, Hiromi forced him to grow his hair out and wear feminine clothing.
This alone is pretty awful, but it gets worse. Nagisa is in class 3-E at Kunugigaoka Middle School, which is where kids with bad grades end up. Hiromi doesn't want Nagisa in that class, but he's happy doing important work with his classmates, so he's against switching out. To force her son to comply, Hiromi drugs Nagisa, brings him to school, and insists he torch the building. In other words: excellent parenting. She only gives up when he saves her from an assassin, because apparently now that he can kick ass, he's worth consideration as a human being.
Ragyo Kiryuin is the antagonist of Kill la Kill. She's also an objectively terrible mother. Ragyo is a seemingly immortal monster, whose body is a combination of human flesh and Life Fibers, which are basically clothing from space. Her goal is to destroy all of humanity and let Life Fibers take over the earth, a goal her older daughter Satsuki pretends to support until she manages to gather adequate forces to take her down. While she's biding her time, she has to endure her mother violating her.
You would think that supervillainy would be enough for Ragyo, but no, she's also aggressively cavalier about the lives of her children. When she mistakenly believes her second daughter, Ryuko, died as an infant as a result of Life Fiber experimentation, she disposes of the body, feeling no grief for anything other than the failed experiment.
Later, she's perfectly content to try and murder both Satsuki and Ryuko for trying to stop her from destroying humanity. Oh, and she orders her third daughter, Nui, to sacrifice her life. Because, evidently, that's just what you do when you're a parent.