- Arc Fatigue: Due to it being a fully-coloured web comic, to say that the story is slow as a result isn't exactly an inappropriate complaint.
- The gathering of the Elements of Harmony and the Carriers of Sin, the webcomic's introduction arc that has started since the beginning of the series around 2011-2012 is still ongoing as of mid-2020. Applejack joining the Mane 6 takes up the most chapters out of the five elements and final Carrier of Sin has yet to even be revealed.
- The fight against Berserker!Spike has gained this reaction over time. Starting at the tail end of Chapter 9 in August of 2018 and encapsulating all of Chapter 10 by March of 2020, the fight has begun to wear on people's nerves due to Berserker!Spike being an Invincible Villain, tanking every attack thrown at them, including one that should have killed them, yet getting right back up and brutally injuring Rainbow Dash, Fluttershy, and Pinkie. Add on the rather depressing nature of the conflict since none of the Elements want to kill Spike, the frustration over Applejack still refusing to help despite Celeste outright begging her at this point, and the months long gaps between pages, and it can be frustrating to read. When it finally ended on June 2020, it was settled without Applejack's help, making people wonder when is she ever going to join.
- Base-Breaking Character: Applejack. Her detractors have accused her of giving up on friendship too easily, while her supporters find her reasonings understandable. Moreover, her detractors have gotten inpatient with her Refusal of the Call, because of how it resulted in two instances of the villains nearly winning, while her supporters believe that her eventual acceptance of the call will be worth it. When the fight against Berserker!Spike came to an end without her help, Applejacks detractors had given up on her, and believe that someone else needs to become the Element of Honesty, while her supporters believe that the victory against Berserker!Spike wasnt meant to be hers, and are still waiting for her moment to shine.
- Epileptic Trees:
- At this point, only one of the Carriers of Sin has yet to have their identity revealed, leading to speculation in the comments. The most popular guess seems to be that he's Cheese Sandwich, given that some of the supplementary materials have included him, the two look rather similar (not to mention his cloak shares Cheese's color scheme), and he apparently has an interest in Pinkie Pie (specifically Pinkamena).
- When the picture of the two Berserker Dragon eggs were shown, some speculate that the second egg is either Torch or Ember due to it sharing a similar colour scheme as them.
- Hilarious in Hindsight:
- This comic being made before My Little Pony: Equestria Girls was even an idea at Hasbro.
- This webcomic had the Shadowbolts as O.C. Stand-in when they weren't even real characters in the main show, just part of Nightmare Moon's magic to slow down the Mane 6. Now comes My Little Pony: Equestria Girls Friendship Games which now has the Shadowbolts as real characters (granted under different names of course), long after this comic did it. Even more ironically they're a sports team, something the Shadowbolts in this series claimed they were when they met Rainbow Dash.
- Perhaps even funnier is that its now been revealed that one of the webcomic's Shadowbolts is Flash Sentry while one of the Friendship Games Shadowbolts is Twilight Sparkle.
- Gilda showing up in the comic not long after The Lost Treasure of Griffonstone aired where Rainbow Dash and she have mended their friendship. It's hilarious as Gilda was revealed by Word of God to be one of the Carriers of Sin, i.e, an enemy.
- The Reveal that Applejack is a Lonely Rich Kid, which means that Apple Bloom is just as rich (if not richer) than Diamond Tiara, meaning that the latter will have one less justification for bullying the former should they appear.
- Even moreso when she finally reveals her reason for not making friends: A bad experience made her believe it wasn't worth it to have any. Not unlike two certain cases in Season 5; Moondancer and Starlight Glimmer.
- And then comes the fourth Equestra Girls movie, My Little Pony: Equestria Girls Legend of Everfree which ended with the Humane 6 and Sunset gaining superpowers. It's like this comic was predicting future events of their movies.
- Nightmare Fuel:
- Pinkamena. Seeing Pinkie go from Genki Girl to acting like a full blown Serial Killer is disturbing enough, but watching her torture her victims by breaking limbs and then pulping their insides sends it right over the edge.
- This comic's version of Flutterbat. Evidently, according to dialogue from Rainbow Dash, Fluttershy turns into Flutterbat every Halloween. Flutterbat is capable of turning people into apples via a sort of magic. The only way you'd be immune to it is if you find a house to stay in and not invite her in. Applejack, unaware it's not a costume, lets her into her house... where Applebloom, Sweetie Belle, Scootaloo, and Spike are in... alone. And Flutterbat has every intention to make them into apples.
- Tear Jerker:
- The Reveal that Applejack is a loner because her only "friends" before were after her money; doubly so since Applejack in the show is such a warm, open, and friendly character.
- Trixie's introduction. She challenges Twilight to a magical duel (not that one) and ends up humiliated in front of an audience for underestimating her. It's implied that Trixie was very confident in her skills and illusions and being shown up by someone younger was a hard pill for her to swallow. She runs to her trailer in a sobbing wreak, only for her night to get worse as her foster parents, the Flim-Flam brothers, tell her to pack her things and leave while under the influence of Discord's magic.
- The Reveal that Fluttershy's mom had her at around 14 and that Fluttershy has no idea where her dad is.
- Unexpected Character: Descent, one of the Shadowbolts turns out to be Flash Sentry of all people.
- Values Dissonance: Pinkie Pie refers to Haze (a guy with dark skin) as "chocolate" at one point and makes a bunch of Double Entendres about it while fighting him. It's might just be a translation error, but still.
YMMV / Friendship Is Magic