The opening scene of the story describes Jaune roaming the battlefield riddled with corpses of his friends and reminiscing about their deaths and how he failed them. Even knowing that Jaune will get an opportunity to change that outcome, it is still painful to read through that.
Just about everything about Emerald's situation. When Jaune meets her for the first time she is utterly broken by her life as a street urchin, to the point where she perceives even basic gestures of caring and kindness as suspicious and every living day as a fight for survival. It takes her months to stop fearing a sexual assault from Jaune and years to start seeing his affection as actual love.
When Jaune tells her he's going to Menagerie and that she can't come with, Emerald has a full-on hysterical breakdown. She starts crying, hitting him, screaming that she hates him, and even threatens to tell Ozpin all of Jaune's secrets if he doesn't reconsider. It ends with her (very reluctantly) accepting that he had to leave, and crying into his shirt while apologizing for threatening to tell on him (which would have landed him in jail, given his mob connections) and that she doesn't hate him.
The White Fang is absolutely heartbreaking in how spiteful its transformation was. In canon, it took years more for them to slowly shift to terrorist acts. Here, because Jaune stopped Tyrian and then moved to Atlas, Tyrian and Hazel infiltrated the Fang and turned them hyper-aggressive three years early to attack the Vytal Tournament so they could try to abduct Jaune. At the very least, in canon, there was a legitimate point to why they turned bad, not just as a source for disposable mooks.
Ghira Belladona's death and the effect it's had on Kali and Blake. Blake jumped off the slippery slope hard and Kali is essentially a broken woman who is the Authority in Name Only of Menagerie, as if she does something the White Fang doesn't like, they'd kill and replace her, then probably use her death to inspire more hatred and fear. And that's only if they decided kill her- they could leave, taking Blake with them, or they could use Blake as a hostage to ensure her cooperation.
Pyrrha's loss to Emerald is the result of her seeing the same incident that traumatized Ruby through Emerald's eyes- and not just through her eyes, but as if she was living it. She felt satisfaction and love for Jaune for brutally killing anyone who tried to threaten her, and she says this all while sobbing to her sister.
Ruby. In canon, she's a very strong huntress who doesn't let anything get her down for very long, The Heart of any group she's part of, and a dedicated leader. In this timeline, she gets traumatized so badly that she can't spend any time in Jaune's presence without hiding behind someone else, and has given up her Huntress dreams altogether.
A big part of the reason Qrow hates Jaune initially is not because he cheated, but because Qrow saw the fight as the last chance he could ever have to get his sister to come home and be with the rest of his team again. When she leaves Qrow later on, he's left standing in shock, one arm outstretched to try to stop her from leaving.
Alexander Nikos is not a nice man, but his attitude is so bad that in canon, it killed his daughters. Helena Nikos, attempting to escape, joined the Specialists but died when she ran into Tyrian (in this new timeline, Jaune accompanied her team. When they ran into Tyrian, all of them together managed to drive him off and get away). Alexander beat down Pyrrha so much that while she became "The Invincible Girl," she was so subservient to authority that it led her right to Cinder Fall and her death.
Jaune holding the Idiot Ball when it came to Blake is one in hindsight. All Jaune wants is his old, dear friend back, and just for a moment he thinks she can be trusted... and she's more violent and extreme than Adam in this timeline.
Earlier, Adam finds out that Blake, who has been his emotional center and that which keeps him from going off the deep end... has been going behind his back the entire time and is reporting all of his actions to Tyrian, Hazel, and Sienna because no one trusts him anymore for the crime of being the Only Sane Man.
While she's recovering in the hospital, he gets a very unsubtle hint that if he screws up or betrays the Fang, they'll kill Blake.
Ozpin notes one at the ball to celebrate the opening of the ASH Gym. Jaune Ashari not knowing how to handle a friendly Jacques Schnee is somewhat amusing. Jacques' oldest daughter not knowing how to deal with a friendly Jacques Schnee is just sad.
Blake. For all her new violent and extremist tendencies, she is genuinely loyal to the White Fang and its message; but Tyrian, Hazel, and Sienna are just using her as insurance to keep Kali from cutting ties with them. If Kali told the Fang to pack up and leave, they'd take her only living family member left with them and then simply have Kali killed discreetly. But even that's not enough, as they send Blake on a mission to capture Jaune. Had she been killed, it's implied that the Fang would have used her death to push Kali to war with Atlas. Once she lands in the hospital after that ill-fated attack, her life is now being hung over Adam's head like a Sword of Damocles- if he plays ball, she lives. All in all, she's completely blind to the fact that the cause she started working with doesn't exist and is using her for its own ends, and all of this on top of her sorrow, pain, and rage at the death of her father.
Chapter 45 reveals that Vernal is so hard on Jaune because he was her first true mentor and she felt betrayed that he simply left her behind without a word then went on to adopt another stray orphan. In the end, Vernal is constantly angry at Jaune and hates Emerald because she wishes she was Jaune's adoptive daughter.
It also rephrases a scene in the previous chapter in a different light- where Emerald and Yang were trying to manipulate Vernal with the idea that the winner of the Mistral Tournament would get one-on-one time with Jaune, they assume that Vernal's just in it for the opportunity to get stronger. With this new information in line, it's a chance for Vernal to get some one-on-one time with the father figure she wishes she had.
It's quite sad then, learning that not only is Jaune thus far is ignorant of Vernal's desire to be his daughter, but that he shamelessly used her as bait to determine whether or not Cinder was working for Salem, and risking her life for his own goals.
Chapter 45 also reveals that despite Winter being incredibly obvious that she wants to be with Jaune, that Everyone Can See It, and that she kissed him on the lips, Jaune doesn't return her feelings. And even if he did, which he doesn't (though he'd be willing to go on a few dates and see how things worked out), he's not willing to put Winter in even more danger since he's Salem's number one target. Which makes things worse for him because if he tries to use It's Not You, It's My Enemies, he runs into the problem of Winter herself. She's not the kind of person who takes "No" lying down, and quote, "A Schnee always gets what she wants." She's also able to hold her own in a fight and has resources to do so. The problem is, that sort of attitude would just get her killed. She might be able to hold her own against the White Fang or raiders, but Salem's forces would bring an entirely new level of pain down upon her that she would be swept away against.
Chapter 46 provides a massive one. It turns out that according to an old lady in Anima, Nora and Ren were found by Watts and would likely be indoctrinated into Salem's cause under his care.
Chapter 54 however confirms that while this is not the case, he has been keeping them imprisoned in cages terrified and alone. It also turns out that the whole reason they wound in so much trouble is that they were searching for the man who saved them in Kuroyuri, Jaune.
As time goes on, the remnants of Team STRQ are starting to lose their faith in Ozpin. It's subtle, but they clearly trusted and followed a man that they liked and respected back when the story started. However, since they've started seeing what happens when you don't just follow along with him (by seeing how Ozpin treats Jaune) and Ozpin's increased interest in Ruby and Yang (despite Summer, Taiyang, and Qrow all telling him to leave them alone multiple times), it's clear a rift is forming between Ozpin's go-to team and himself.
After Jinn reveals to Raven that Jaune is from a Bad Future, she is understandably upset with Jaune for keeping the truth about the fate of the world (and her daughter) from her, but seems even more disappointed in her other self for essentially running from the fight altogether.
She goes as far in the next chapter to refer to her other self as a coward.
Summer's reunion with Raven starts with her delivering a slap and deteriorates from there, with Summer pleading for Raven to give her an acceptable reason for abandoning them all for fourteen years. She tears into Raven for running away and then later breaks down sobbing and hurt.
Raven doesn't come out of it unscathed either having had all her flaws and their consequences thrown in her face by the only two people on Remnant she considers her friends. She starts angrily chopping down trees before she resolves to prove that she is in fact not a coward.
Summer's breakdown in the wake of Raven leaving and confronting Jaune is pretty bad as well. Jaune lays out (in his own way) why he doesn't trust Ozpin, and why he doesn't think that Summer should either. Summer fights back, but Jaune goes way below the belt when he gives her his frank opinion that STRQ wouldn't be nearly as messed up if Oz hadn't meddled. He points out that Raven ran away, claiming not to care about anything but still cursing Ozpin's name fourteen years later. Qrow was forced to choose between his old and new families. Tai and Raven's marriage ended in disaster, and Summer has been put squarely in the eyesights of those who want to exterminate those with Silver Eyes.
The beginning of the end is when Jaune reveals Ozpin's true plan- he wants to make Ruby into the next Summer Rose and her, Vernal, Yang, and Emerald into the next Team STRQ to replace STRQ when things go bad. Even if Ruby doesn't want to be a Huntress. Summer is appalled, but it’s the fact that she can’t find it in her to say that he’s wrong that shows just how much of a Broken Pedestal she has for Ozpin now.
Jaune unexpectedly finding himself meeting Nicholas Arc. He internally repeats that the man isn't his father but someone else, Jaune already lived a life as an Arc and that would be better to stay away... But he just wants so badly to see him, and his mom and sisters.
Jaune's reasoning for massacring the White Fang despite Hazel's insistence that no one had to die: He's the one who caused them to become such extremists so it's his job to "fix things".
After Jaune and Winter dismantle the White Fang, Blake is shown to outright hate Adam, blaming him for the White Fang's downfall.
Young Jaune and Emerald eventually learn who Raven is and what she did to Yang and to say they don’t take it well is an understatement. While Emerald was never her biggest fan, Jaune viewed her as a guardian angel and his fairy godmother. The fact that Raven never denies what she did emotionally breaks him and he ends up bawling his eyes out in front of his teammate.
Pyrrha's state in Chapter 101. While recovering from what she believes to be an assassination attempt, she's tricked by Lionheart into being captured by the new White Fang. By the time Jaune and Summer find her, she's been tied up in a box, damaged to the point that she can barely stand up and unable to get out of her restraints due to her aura being mitigated by Tyrian, all while she has no idea if her sister and father are still alive. In very short order, she's gained new powers she has absolutely no understanding over, been almost killed, been betrayed by her former headmaster, kidnapped by hostiles, and locked in a box with her family's fate unknown. It's a miracle she even manages to smile during her talk with Summer afterwards.
Chapter 167 has one for both of the Schnee parents; Jacques took a beating attempting to save his family, whilst when shown the future with the Relic of Choice Willow chooses her daughter's life over her own. Doubles as Heartwarming, especially considering how the pair are in canon.
Despite Salem being held as the central apex of causing misery throughout all of Remnant, as she is on the verge of death she mentions that even if she dies, the Kingdoms will eventually destroy themselves, and also just how miserable and wretched her life has become ever since the Brother-gods of Light and Darkness cursed her with immortality and Ozma with his eternal soul-based parasitic life, she asks for Jaune to finally put an end to the endless nightmare she's endured for countless millennia. He complies. Also acts as doubly-sad as his current self was constructed from his original timeline's Salem with the help of all four Relics, of which the current Salem realizes as she feels that the Jaune next to her will very soon disappear without her magic to sustain him. As he's about to disappear, she gives him the last of her magic that lets him remain for another month or so, then he will be gone just as she soon will be.
