Izzy becomes depressed at being left out of Zipp's wingball game and ruining Hitch's nature hike. It's really depressing to see somepony as cheerful as Pinkie Pie look so sad.
The state of Canterlot as seen at the end of Issue #1 and within Issue #2 itself. What was once a bright beautiful city that represented the rule of Princesses Celestia, Luna, and Twilight is now nothing more than a bunch of decayed old ruins. Sunny is heartbroken to see what has become of it.
Sunny: I always saw Canterlot as this perfect beacon of friendship, a place where unicorns, earth ponies, and pegasi lived in harmony and nopony ever felt left behind.
Izzy: That's what you wanted to create in Maretime Bay.
Sunny: Yeah. But seeing Canterlot like this... makes me question how hard it would be to keep it that way.
Discord's current situation. He's a depressed, aged shadow of his old self who lives in the remains of a lost city, with only a few small animals for company, and no longer believes magic is a good thing; to the point that he's willing to destroy all of it to keep the peace. It's clear that he was never the same after Fluttershy passed on a long time ago.
Issue #9 has the Mane Five arguing about what to do about Discord destroying all the magic in Equestria. It hurts to see such good friends at each other's throats like this.
What's even more ironic is the covers for Issue #9 feature the Mane Six smiling happily. While the friendship between Twilight and her friends isn't perfect — as they had their fair share of fights and arguments — they usually get along great, which makes what's going on in the issue itself so much more jarring.
Discord shedding a tear from seeing Fluttershy's message, which she recorded for him before her death. It's clearly been a long time since he last heard her voice or saw her face, and it takes everything he has for him to even look at Fluttershy again. The moment is made even more powerful by her spirit embracing Discord as she gently reassures and reminds him of their time together and that he is still capable of good.
Discord: (tearing up) I can't see this again. I can't see her. Please don't make me watch.
From Issue #11: The story of Nagathine "Naggie" Irons. She lost her parents in a tornado and was sent to live in an orphanage. Not only that, but she was also the victim of a mean prank where her "friends" supposedly were going to throw her a birthday party, but never showed up.
Issue #12: Dahlia and Pansy Silverbell's friendship became frayed after Dahlia started resenting Pansy for always winning baking contests. This even led to Pansy temporarily leaving Maretime Bay.
Issue #14:
Violette Rainbow has spent her whole life being ostracized by others for the miscolored patches on her coat.
When Violette visits Izzy in Maretime Bay, her clumsiness causes mess after mess, ultimately causing Posey and Pipp to yell at her.
When a "chance" meeting with two zebras gives Violette some hope for a normal appearance, she takes all of their potion instead of a small amount as instructed, resulting in her coat taking on random colors and patterns (thus making her even more unnerving to other ponies).
Issue #18: Zipp loses the support of her fans due to Carotang's machinations, and Pipp's decisions make a mess of the royal dining hall. Both sisters feel like failures because of this.
