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.
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.
Fridge Brilliance: 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.
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.
Twilight's first encounter with the Invaders: a Chryssalid massacring three people in front of her, then attacking her.
Twilight's response to it, crushing it into a pulp (they literally had to vacuum pump it out of the crater) with her telekinesis, is also this. In-Universe, even for Twilight herself.
Twilight waking up in the X-Com containment unit, about to be "interrogated".
Twilight's own nightmare where she repeats her killing of the Chryssalid, only it turns into Spike, plaintively asking why she's killed him.
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.