These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Arads Stardust
Ascended Fridge Horror: Seems to be the case in in Fortitude Amicitia. In chapter 31 of Stardust, Celestia asks why Discord doesn't "release her", clearly implying that he has sealed off some of her powers, so that she can protect her ponies from the oncoming invasion. Discord refuses, because she would end up falling into her own corrupt rendition of Order, which would result in her petrifying every living thing in Equestria, complete with showing a corrupted Celestia atop a pedestal of petrified ponies and surrounded by dozens more for emphasis. In the very first chapter of Fortitude Amicitia, reference is made to discovering prison-vaults filled with tens of thousands of petrified ponies, petrified for the most minor of crimes by a "Queen Solaria". Upon the discovery, Celestia immediately cancelled the expedition and arranged for the professors to forget about it in exchange for comfortable jobs. The reason why? "Past sins should stay buried and forgotten", as she puts it. So, the implication is pretty clear that Discord sealed Celestia's power and won't unseal it because she has been an Order-mad tyrant in the past when she had full access to it.
Lana has become this. First was the arguing over whether or not her Shipper on Deck "joke" and/or her general antics in the name of "fun" made her The Scrappy but, since chapter 20, when her "joke" has come out and she's been given a What Were You Thinking? chewing out, only to explode back, it's gotten worse. Some see her as sympathetic and understandable, others see her invoking a Freudian Excuse as the reason why its Never My Fault.
The introduction of magitek gear in chapter 26 made some readers iffy.
Some readers were also displeased by Twilight's Unstoppable Rage and the subsequent Curb-Stomp Battle she issued in chapter 33, thinking her overpowered and rendering the others worthless. Other readers stepped in with counterarguments and reasons why the feat fell within previously established ballparks.
Happens again in chapter 34 where the ponies overzealous reaction upon discovering X-Com in Equestria when they were returning Twilight left a fair amount of readers in disbelief.
Fortitude Amicitia has become this amongst the fans, many of whom disapprove of the crossover, especially since the characters from The Dusk Guard Saga won't even be reappearing in Mente Materia themselves.
The supplemental info often mentions how there have been a mysterious string of disappearances where people with backgrounds in the military, science and engineering just vanish from their homes with no sign of struggle. They aren't being abducted by aliens, they're being recruited by XCOM and agreeing to the absolute secrecy requirements.
In Mente Materia it seems that the worst political pundit in the world managed to get the opportunity to confront X-Com for their unsanctioned military actions and covert alliance with an alien race. Considering the influence of the Council, that is implied to include at least the Vice-President of the United States, it's possible that they deliberately allowed the leak to reach Senator Coleman specifically, so that he would make any opposition of the X-Com project a joke in the eyes of the general public when it inevitably became public knowledge — someone more competent could have presented rational and crushing arguments against the organisation's existence in its current form and seriously hindered their current operation model.
Fridge Horror: After The Reveal in chapter 28, one has to wonder: just why have so few humans been able to access the Field to this point? Also, when Twilight describes the Field, she describes it as feeling like it hasn't been used in a long time... could it be that there were once more people who could use it? If so, where did they go? And why?
More than one fan has accused the Council of holding this after The Reveal in chapter 15, pointing reasons why it makes no sense and is even actively harmful for the Council's purposes. Perhaps not coincidentally, the next chapter shows the Council's debate over what to do with Twilight, with some members clearly against the plan, and reveals that the current "prepare a special base for more extreme measures, but leave the decision to send her there to Commander Bradford", to be the result of non-unanimous consensus.
All of X-Com gets hit with this when a Council inspector visits to receive the latest monthly report. Despite sporting iffy credentials and his presence being an unannounced break in the usual method of how X-Com reports their progress, no-one keeps watch on him as he is allowed free access to all facilities and top secret files inside the base. He quickly turns out to be an EXALT spy.
Rescued from the Scrappy Heap: Vahlen may be on the path to this after the events of chapter 17, with hints of her reasonings for being so antagonistic towards Twilight being confirmed from chapter 15.
Dr. Vahlen, for most of the readers, due to her antagonistic approach to Twilight.
Lana started becoming this for readers when she decided to take her Shipper on Deck reasoning as an excuse to troll both Matt and Twilight, continually harrassing the former to the point she puts a doctored photo of Twilight in his locker and refusing to stop despite requests by Matt. It's gotten to the point Twilight has "muted" her twice out of sheer exasperation. She gets called on it in chapter 20, with mixed results.