Lyle definitely crosses it in “Lyle’s Last Stand”, where he kidnaps Lincoln, Lisa, Lucy, Luan, and Lola and takes them to an abandoned warehouse, with the intent of killing them, while also using them as bait for Ryan and Lynn. While he might have been under the influence of a Psycho Serum, his past behavior heavily implied that he was already a budding sociopath anyway.
Though only revealed much later, Kathleen crosses it at the start of “Candy Stripers”, where she intentionally shoves a skateboard under Renee’s foot and makes her fall out of a second-story window in order to get rid of her, not caring one iota if she died or not, and latter dialogue implies that she was hoping that the fall would be fatal. Though if the backstory about how she was forced by her father to fund and host charity events is to be believed, she has pulled far worse stuff in the past.
Flip crosses it the minute he entered the story, by feeding Lana drugged candy with meth-like qualities that made her go on a crazed rampage, all so she could serve as a distraction while he stole a cash register to help pay his mob debts.
Unintentionally Unsympathetic: Rita was meant to be seen as a struggling mother with an unprepared husband and dealing with a bunch of self-centered and spoiled daughters, but her clear favoritism towards Lincoln, the fact she wants to take advantage of Kathleen's "generosity" despite knowing she isn't completely trustworthy, and even calling Lynn Jr a burden makes her come across as a spiteful woman who put more than she can chew in her mouth and refusing to see her own role in this chaos, all while being too cynical to see that some of her daughters are changing for the better.
The story makes it clear how miserable Lucy’s life was prior to the start of this story. Growing up, she was generally ignored by her family (except for Lincoln) and ostracized and bulliedby her classmates and even her own sisters for her creepy looks and strange interests, leaving her with no friends and even a crippling fear of socializing, as she has become conditioned to being shunned and ridiculed. Fortunately, she finds a Cool Big Sister in Luan and her first real friend with Ryan, and her bond with Lincoln remains as strong as ever.
Speaking of Luan, her situation was just as bad as Lucy’s, with both her peers and family shunning her, on top of being the favorite target of Kathleen Tisdale’s relentless persecution and bullying. This has left her with a myriad of visible issues that repeatedly surface behind her goofy persona, revealing her to be a Sad Clown, and it’s implied that her nonstop pranks (including her annual “Prankmageddon”) were just desperate pleas for attention. Things get even worse for her over the course of the story, as her sisters become fed up with her antics and start scornfully mocking and belittling her, before subsequently hobnobbing and shamelessly sucking up to Luan’s tormentor, because she has lots of money, not caring about how it affects Luan herself.
As explained already, the story puts Lisa’s through multiple wringers, leading to her depression and self-loathing, leaving her even more sullen and joyless than even Lucy. To make matters worse, both of the two main disasters involving her experiments were entirely out of her control, as they were instead (accidentally) set into motion by Leni and Lola respectively. This culminates in her actively trying to commit a Death of Personality in order to be normal and keep her family safe, something Lincoln and his team are completely unaware of.
Lincoln qualifies as an Iron Woobie. While he used to have a fairly standard life for a kid his age (his frantic and chaotic homelife notwithstanding), after “the incident” in the original timeline, he saw his parents divorce and his family being split in two. Now he works feverishly (if not obsessively) to change their future for the better, and while he and his team have had success (to an extent), in doing so, they had to go through multiple life-threatening and mentally-scarring events, especially in regards to their numerous brushes with Lyle, One Eye and Lisa’s crazy experimentsgoing haywire. While Ryan, Lynn, and Lucy deal with it better, all of this has left Lincoln visibly traumatized but he still tries to keep his composure and barrels onward.