The first thing the audience sees Madison do after being resurrected a second time is smoke a cigarette. This calls back to her first words after being resurrected in American Horror Story: Coven, I need a cigarette. As Madison was a heavy smoker in life, its likely one of the worst aspects of her Hell was being an addict denied cigarettes, hence why she immediately smokes after being brought back to life.
Coco and Mr. Gallant make several comments alluding to or directly stating that Mallory is a terrible assistant to Coco, and initially it comes off as the two of them being catty and mean-spirited, but come the reveal that Mallory was a completely different person and had an identity spell placed on her- as did Coco, to a lesser extent it seems- she might genuinely be bad at being an assistant.
It is revealed upon Michael's arrival that Miss Venable and Miss Mead have gone rogue and have simply been making up the Outpost's rules this entire time.What is the highest color in the Outpost? Purple. And what did Myrtle say after bypassing Miss Venable before the apocalypse begun?
Myrtle: Purple is for royalty, dear, not middle management.
Pay attention to the soundtrack to the opening credits, and you can hear Venable's cane as an auditory effect.
How did Cordelia know so fast that Michael was evil? He literally walked into a place "Where the light from which we all draw our powers is extinguished" and retrieved Queenie. Cordelia couldn't do it because it was a place wholly ruled by evil - which means that for Michael to achieve what she could not, his power came from a dark place.
Cordelia decides to put Coco and Mallory under identity spells that place them in roles of scorn and subservience, respectively, towards one another in order to diminish Mallorys confidence and therefor suppress her Supreme powers. This is exactly what Fionas emotional abuse of Cordelia had done to Cordelias own powers.
Madison's one-woman bravery in standing against Michael, armed only with Mead's robotic arm could be put down to her character development in becoming more of a team player, but also down to her knowledge of Cordelia's plan. Either way, Madison was screwed. If the plan succeeded and Mallory reversed time, Madison would end up back in Hell. If the plan failed and Michael slaughtered all the witches, guess where she'd end up? Hell. She quite literally had nothing to lose.
In Fire and Reign, the witches in the Coven are caught unaware when Michael and Ms. Mead show up (after Dinah breaches Cordelia's 'aura shield' protecting the Academy). Apparently, the witches never considered that someone would have figured out a way of detecting the shield and breaching it (which is a case of Too Dumb to Live, when you consider that they fought the voodoo practitioners five years earlier and they attacked the academy then) - and thus, they never set up a warning signal to alert them if the shield was breached.
This also acts as Harsher in Hindsight when looking back at Madison's insulting the resurrected Dinah in Forbidden Fruit and saying that her backward voodoo shit couldn't help defeat anyone - because it was Dinah's powers that allowed the Coven to be all but wiped out by Michael, and the implication was that if not for her, he wouldn't have been able to get to the witches.
Michael's actions towards Mr. Gallant in the earlier episodes become much more disturbing upon seeing Michael's relationship with his father Tate, whom Mr. Gallant heavily resembles. First off, there's Michael being seductive with (and possibly even sleeping with) a man who looks like his (biological) father, and then there's the way he tells Gallant that he would never sleep with him. It makes one wonder if Michael has daddy issues that he's taking out on Gallant.
Thanks to Mallory changing history, the Coven now has no reason to return to the Murder House meaning that Tate and Violet have not reconciled and Moira is still trapped there and not reunited with her mother in heaven.
Also, while changing the timeline resulted in the Coven and the world being saved, it also means that their past enemies have been brought back to life. Along with Mead and her satanist entourage who manage to find their new Antichrist in 2024, there's also Dinah Stevens, Ariel and Baldwin, and Jeff and Mutt. And while it'll be a long time before any of them poses a threat to the Coven or the world itself, they all just need the right motive to kickstart their sinister schemes once again.
To be fair most of the horror is mitigated by the fact that Mallory kept all the erased timelines memories, she knows who Mead is, she knows Ariel and Baldwin are misogynistic psychos, she knows Dinah would screw them over at the drop of a hat, the Coven will probably be informed and at least have things in place to stop most of what went wrong the first time around if things play out the same in any way.