Littlepip's overly humble attitude makes more sense and feels a lot less like a cliché good guy trait when you remember that, back in Stable 2, she had no friends; the only thing she could do to pass the time was clean up a room, occasionally fixing a PipBuck or two; she's a lesbian and it's very likely no other mare in the Stable swung that way; her mother was a neglectful alcoholic; and, as she pointed out early on, her cutie mark was of quite possibly the most common piece of equipment in the Stable. She probably didn't have even a shred of self-esteem when she walked out the door. And out in the Wasteland, being forced to kill to survive made her feel like a monster as opposed to a hero, so she couldn't even take pride in her victories.
Silver Bell had a balefire bomb right in her barn for who knows how long. An armed balefire bomb at that. And she's a child. One little slip up, and...
Slip up, shmip up. It was pretty heavily implied that she knew exactly what it was and was planning on committing suicide with it after one last, big party.
It is horrible and sad to see a little child so hurt like that though. Even pre-apocalypse it was hard to help everyone, and that was with a widely established security/police force, and with the Ministries. Anything. But in the Wasteland, even little kids have to put up with adult-level hell-on-Earth grade things, and can't really ask anyone for help, even if they're nearby, because everyone's probably got the same problems in the Wasteland. The doctor in Fallout 3 town Megaton tells outsiders they'd better be dying before they ask for help, that he only wants to spend medical resources on people he likes. Pre-War they'd get slapped with a lawsuit for that. Post-War, people gotta take care of themselves, and resources are even scarcer.
In chapter thirty-four, a dying bandit tells the people of Arbu, "You can't... have... my son..." This seems perfectly normal, until it's revealed that the ponies of Arbu are cannibals. What's more, according to Grandpa Rattle, a good portion of the aforementioned bandits are former residents of Arbu. The dying bandit knows what they're doing. He isn't saying, "Don't take my son." He's saying, "Don't eat my son."
A bit of Fridge Horror for the Fallout: Equestria series as a whole, but... Pretty much everything that came after season one is uncounted for. Discord, Chrysalis, Sombra, the Crystal Empire, Tartarus, what the hell happened to those? Were they unaffected somehow, or did the balefire completely break them?
Furthermore... Tirek is out there, somewhere. A magic-sucking monster in a world where literally everything is saturated with magic. If he's broken out of Tartarus, he'd have the chance to become a god.
Near the end, Discord is briefly glossed over. Best case scenario, his power was so little because of the events that he ended up shrinking to a tiny irreversible size and now puts random things in trash cans and other pointless things (random drops). Worst case? He was still a statue when the bombs hit. Of course, it's not particularly important to the story and they're just theories that were thought of by random, unnamed characters, so his fate is still ultimately a mystery.
Now, we know that Chrysalis has a throne that nullifies magic in and around her hive, which is also situated on an island a decent distance aeay from the mainland. The Changelings might actually be the one species completely unaffected by the war, as any after-effects of the megaspells that managed to reach all the way to their island would get nullified by the anti-magic field. Though, with their food supply having just been blown up, it's unclear how long that would last... It's still a bit funny to imagine Chrysalis being in the middle of drafting up a plan to infiltrate Canterlot when she looks out the window and notices the apocalypse descending onto the mainland.