Emma Frost's father was cold and emotionless and encouraged his children to play mindgames with each other. Her mother was a neglectful drug abuser.
Magneto, especially in his early days, dips into this in regard to his children as his life as a father has been far from spotless. Quicksilver has gotten the brunt of his cruelty, as apart from rarely giving Pietro affection or praise, Mags nearly kills him in House of M as Scarlet Witch pleads with him to stop. Wanda herself also got plenty of manipulative emotional abuse from him and her unstable nature can definitely attributed to his upbringing. He’s also come into conflict with his biological daughter Polaris who fairly points out how much he sucks at parenting. Thankfully most comics have toned this down, with Magneto being presented as a protective and caring father and grandfather. Mostly to Lorna, Wanda and her sons Wiccan and Speed, but even then, he's far from perfect and often puts his own schemes over them.
Many fans forget, but Mystique is a terrible, terrible, downright awful mother let's start with her biological son Kurt Wagner a.k.a. Nightcrawler when he's born she was cast out by the village by a mob. At first, she seems like a Mama Bear protecting her baby from harm until she realizes she can use her powers to make a new life and there’s only one thing that's holding her back and she tosses little baby Kurt off a cliff◊. Mystique says she doesn't regret it when confronted by her son and even flashes him a grin as she says so note Keep in mind this was the original telling of Kurt’s origin, X-Men Origins: Nightcrawlerretcons the events having Mystique tie baby Kurt to a log and sending him down the river before collapsing in exhaustion, perhaps in an effort to make Mystique less monstrous .
Despite tossing him as a baby and frequently fighting him, numerous writers have tried to make amends between the blue mother and son. Mystique has hesitated when given a chance to stab Kurt, begged him for forgiveness and even sacrificed herself for him, but the rest of the time, she just manipulates him for personal gain or takes out her rage for Azazel (Kurt's dad) on him. The fact that Nightcrawler is willingly to be kind to her, protect her and even reluctantly accept her into X-Men speaks more about Kurt's compassion than it does about her. Averted in AXIS; due having her morals flipped, Mystique loves Kurt unconditionally and does everything in her power to make sure he doesn't do anything he'll regret while he's evil, she even grabs onto him while he tries to bamf away from her saying that she loves him. However, this is actually more upsetting, as it proves Mystique has the capacity to be good mother but just chooses not to.
There's also Mystique's treatment of Rogue, her surrogate daughter, and if you thought Nightcrawler got the worst from her boy you'd be wrong. Raised from a young age with the worst anti-human teachings, Rogue took after Mystique and also received abuse from her and was abandoned (she really has a knack for it) leading to Rogue finding the X-Men and raised in a better fashion. Like with Nightcrawler, the writers bounce back and forth with Mystique's care for Rogue sometimes she’ll be a Mama Bear and willingly to sacrifice anything to protect her daughter. But at other times she has slapped her daughter◊, stabbed her in the gut◊ and shot her◊. If that weren't bad enough, there are Mystique's "attempts" to look after Rogue like turning into her to seduce her boyfriend Gambit to see if he'd be faithful to her daughter and even kept up her record of terrible baby handling as she tried to use Hope Summers to try to revive Rogue from the Strain 88 virus and gets "The Reason You Suck" Speech from Gambit. When Rogue wakes up and learns from an overjoyed Mystique what she tried to do, Rogue wastes no time giving her mother a beatdown.
We also can't forget to mention Graydon. It's sad when Mystique is a worse parent than Victor Creed. She & Victor were lovers for a while, and Mystique faked her death to run out on him, and didn't bother to ever tell him she was pregnant with his baby. When said child was born, Mystique kept an eye on him until she found out he wasn't a mutant, then lost all interest in him, describing him as boring. Graydon sometimes snuck away from the orphanage to spy on her, where he discovered her true form. After finding out who she really is, Graydon is shocked & Mystique proceeds to taunt him about it, then reveals Sabretooth is his father, rather than a bond trader like she said. Even into Graydon's adulthood, Mystique cares nothing for him and mentions abandoning him because a kid would've cramped her style. Not to mention she was the one who assassinated him. But prior to the assassination, is it any wonder he has a low opinion of mutants?
Amazingly, Sabretooth, unlike Mystique, did seem to have respect for their son after seeing how ruthless Graydon could be. Victor teases Graydon, but seemed genuinely fond of him, to the point wishing him luck on his campaign & asking his son to remember him when he becomes president. He also claims Graydon as his son, given he frequently calls him "son" whenever he addresses him. When Victor & Mystique come to blows in X-Factor, Mystique shape-shifts into Graydon as a way to distract (or possibly hurt) Victor, as she did earlier when she morphed into his dead mother to upset him. Only this time, Sabretooth was beyond pissed and wasted no time clobbering her for it. During their stint in Hell during Weapon X (2017), Sabretooth is horrified to find Graydon in Hell and immediately tries to save him. He is visibly appalled when he pleads with Mystique to help him save Graydon, and she coldly tells him to just leave Graydon in Hell. You could even argue Sabertooth's abuse was his twisted way of caring. When we do see him given a flashback his parents are cruel, but with good intentions, honestly thinking Victor was possessed. His kid would have to be tough to survive such a world and to already have no powers as a handicap.
Wolverine lampshades it when he's listing how bad Mystique is, as he calls her a "piss poor mother" and this coming from a dude who has dozens of illegitimate children is very telling.
Wolverine's archenemy Sabretooth had an abusive father. Part of Sabretooth's mutant powers is his canines growing into fangs and fingernails into claws. After his powers manifested, his father chained him up in the basement and pulled those out with pliers. Since rapid healing is part of Sabretooth's powers, they had grown up by the next day, so his father repeated it again and again and again and again. In addition to physical torture, Creed was psychologically abused as well, with his father calling him a monster & even saying he's glad his own father is dead so he doesn't have to see what kind of monster his son gave him for a grandson. He would bring Creed food like a dog and make him beg for it like a dog while calling him a monster. Is it any wonder when Creed finally got loose, his first order of business was to murder his father. Though he won't win father of the year, Sabretooth was a considerably better father than his own. As noted in Mystique's section, he did have some respect and fondness for his own son after seeing that Graydon was just like him in terms of ruthlessness and vindictiveness.
Tabitha Smith/Boom-Boom was abused by her father until she ran away from home. This is a pretty commonplace trope for mutant characters.
Wolfsbane's father Reverend Craig Sinclair helped a group of religious fanatics brainwash his daughter into a programmed killer to be sent after her teammate, Angel. It blows up in his face in an ironic way. Given the level of emotional abuse he subjected her to growing up (his hiding the fact that it was he that sired her upon her supposed harlot of a mother being the least of it) and his leading the mob that shot her and tried to burn her at the stake when her powers kicked in, the above shows that he's nothing if not consistent.
Wolverine had an abusive mother. Elizabeth Howlett Hudson was neglectful of her son as she became mentally ill after witnessing her firstborn son John's claws emerge for the first time, leading to her scarring (her absences were to the asylum); in her few visits to the Howlett Estate, she isn't seen interacting with James. However, after history repeated itself with her youngest son (who had just witnessed his stepfather murdered and had just slain his biological father in his rage), her response was to smack her son across the face with her lover's rifle and disown him, calling him an 'animal' as he fled the estate.
Wolverine's biological father Thomas Logan was also never a saint, although not abusive to John specifically; he regularly beat and abused his other son, Dog, and introduced the boy to alcohol while encouraging the boy's sociopathic tendencies.
X-23 (Laura Kinney) can certainly be considered a victim of this trope, depending on how you define "parents". Zander Rice was one of the lead scientists involved in her creation, and the abuse he leveled at the poor girl was outright horrific. Her mother, Dr. Sarah Kinney, (who provided the surrogate womb and some genetic material) was under the orders of Rice and project leader Martin Sutter to deny X-23 an emotional connection. To her credit, though, Kinney defied those orders whenever she could, but couldn't prevent the emotional damage the young Laura sustained before she could be freed from the Facility's control. And let's not even get into what Kimura, her other primary adult "role model", did to her...
Hints dropped throughout X-23: Innocence Lost (including a copy of an actual police report) and Target X reveal that Sarah herself was abused by her father, which neither her mother nor sister would corroborate, ultimately resulting in Sarah cutting off contact with her family and only briefly reconnecting with her sister before her death.
Kimura was also the result of a neglectful mother and abusive father. Her grandmother attempted to undo the damage, but by then it was too late, and Kimura used the abuse and bullying she suffered as a child as an excuse to do it back to others when she grew older, particularly Laura.
William Stryker in X2: X-Men United lobotomized his mutant son Jason and reduced him to a wheelchair-bound source of mind control serum. He even stops referring to his son by name, calling him "Mutant 143". Xavier is horrified that William would do this to his own son, but William claims that his son is already dead, just like the rest of mutantkind.
In The Wolverine, Shingen Yashida is seen slapping his daughter early on, and later tries to kill her.
Western Animation
Found in one episode of X-Men: Evolution when we learn that Tabitha/Boom Boom's father was a con man who routinely pressured her into using her powers to help rob banks and/or run scams.
◊. Mystique says she doesn't regret it when confronted by her son and even flashes him a grin as she says so note .
