* AccidentalInnuendo: Similar to [[Series/MyLittlePonyFriendshipIsMagic the show]], the comics are getting in on it too. Take a look at this one [[http://www.derpibooru.org/413632 scene from the comic]] without the rest of the page to put it in context.
* AlternativeCharacterInterpretation: While things in the show could always be a bit quirky with the pony population's [[HilarityEnsues antics]] and [[EasilyForgiven the general lack of consequences]], they come to a head in ''The Good, the Bad and the Ponies'', as Equestria can be seen here as a CrapsaccharineWorld whose cute exterior belies a horribly dysfunctional legal system that excuses things like assault, vandalism, extortion, arson, kidnapping, impersonation, hostage-taking, and fraud, but vandalizing a historical site, even one declared so about under dubious circumstances, could get those just ''associated'' with you thrown in jail. Essentially valuing the letter of the law over innocent people's lives, and having no provisions to deal with dangerously violent criminals.
** The Deer in the Root of the Problem arc. It's hard to tell if the forest is attacking Ponyville and Canterlot autonomously, or if the Deer deliberately steered the new growth towards who we know to be innocent people. Combine this with FantasticRacism, some interpret them as ecoterrorists at best, and militaristic warmongers looking for an excuse to invade at worst.
* AngstWhatAngst: The Cutie Mark Crusaders don't seem to think being fillynapped by a monstrous Queen is a big deal. Also Fluttershy is gleefully fascinated by two creatures fighting over the right to eat her and her friends.
* AntiClimaxBoss: Chrysalis gets taken down surprisingly easy, all things considered.
* {{Anvilicious}}: "Root of the Problem" features just as heavy-handed a GreenAesop as any similar '90s kids film you could name, complete with the Mane Six being inexplicably eager to knock down trees to solve their problems so they can get lectured by the deer and a villain right out of ''WesternAnimation/CaptainPlanet''.
* AuthorsSavingThrow: For those who thought Babs Seed was too EasilyForgiven in her debut episode, her portrayal in issue #22 as feeling like she has to constantly prove she's no longer a bully should go a long way.
* BaseBreaker:
** Princess Celestia in the reflections arc (issues #17-20). For some, her actions has driven away any amount of sympathy she might have had while others are fond of her relationship with Mirror!Sombra regardless. What prevents her from reaching full-on [[TheScrappy Scrappy]] status was her MyGodWhatHaveIDone moments throughout the comic... [[spoiler:That is until it's revealed that her travels to the other world is causing the destruction of ''both'' worlds. For most, this just brought her to the scrappy heap. Wether her willingness to [[HeroicSacrifice sacrifice herself to fix this]] and losing Mirror!Sombra (who took her place) as consequence redeemed her is hotly debated]].
** Some readers don't like that Luna behaves in a much more childish and less serious way than in the show. Others find it makes her more endearing and humorous to contrast the straight-laced Celestia better.
* BrokenBase:
** The quality of the comic; some enjoy it for its WorldBuilding and having stories and content the show itself wouldn't dare try to get away with, while others describe them as poorly written fanfiction. Numerous [[DependingOnTheWriter differences in characterization]], a different tone from the show, and the extremely heavy-handed references (both to the fandom and other media) don't help matters.
** The existence of the Nightmare Forces for some, who prefer the idea of Nightmare Moon being a corrupted Luna rather than a different entity possessing her, feeling it cheapens her StartOfDarkness. There's a HandWave they do this via MoreThanMindControl, so Luna's fall to darkness could still be be in part because she was corrupted by her own dark emotions, and thus leave the tragedy intact. Wether it does so or not is a matter of debate.
** The first Annual issue showing more of pre-redemption Sunset Shimmer also got this. While it gave her much-desired backstory, it showed her as already just as bad as in ''EquestriaGirls'', disappointing those who hoped she would be given a FreudianExcuse or reason to believe her HeelFaceTurn was real or deserved. The 2014 Holiday Specials focus on Sunset having to further prove her reformation [[AuthorsSavingThrow came off as an attempt to address that]], but created its own regarding wether or not her treatment during it was justified.
** The Reflections Arc, full stop. Some like Celestia's romance with Mirror!Sombra, others feel it was a case of StrangledByTheRedString due to being poorly written, or that romance shouldn't be in the series. Some loved the ending as a tragic end to the romance, others cried it was a DeusExMachina and seems to be an inter-dimensional invoking of StatusQuoIsGod. There's also the Mane Six [[{{Flanderization}} being Flanderized]] and shoved aside to focus on the Celestia and Sombra romance, Star Swirl's personality not fitting what the cartoon established about him (particularly Celestia's claim "he did not understand friendship"), and the alternate world actually not being explored much, with the alternate incarnations of characters beyond Sombra, Luna and Celestia only being inconsequential cameos. There are also fans that thought the first issues were fine, but the final issue was an AntiClimax and wraps up with no significant CharacterDevelopment for Celestia and the mentioned DeusExMachina ending.
** The Cattle Rustlers arc (#25-26) quickly establishes that Twilight will not use her powers directly against any non-magical citizen of Equestria, otherwise the situation would be resolved in just a few panels (this is even lampshaded in the second issue). This has created debate if that's a legitimate approach to considering her magical strength. Not helping this is the fact that in a previous issue from the "My Little Pirate: Friendship Ahoy" arc {Issue's 13-14} actually did have her use magic on hostile ponies, with claims of self-defense being debatable.
** Writer Tedly Anderson became this due to a highly questionable cameo and some comments he did on some forums and tumblr following the 2014 Annual. The highly polarizing 2014 Holiday Special certainly didn't help. On the other hand, the Manehattan Mysteries arc and the Micro and Friends Forever issues he has written were generally liked.
* CantUnhearIt: Naturally, anyone who watches the show has claimed they can easily hear [[Creator/TaraStrong Tara]], [[Creator/AndreaLibman Andrea]], [[Music/HeyOcean Ashleigh]], [[Creator/TabithaStGermain Tabitha]], [[Creator/CathyWeseluck Cathy]] and other voice actors from the show when reading their respective characters' lines.
** In case you need help, [[http://www.youtube.com/watch?v=93g_LAAHLXs here]] is Creator/AndreaLibman reading the "Nature is so fascinating..." scene from Issue #3.
** This can get awkward in the second Annual issue, where the Power Ponies have rather different personalities to the Mane Six.
* ContestedSequel: The Nightmare Arc (Issues 5-8) was this to the first arc for having more drama and action at the expense of humor and characterization, and the {{Retcon}} to Nightmare Moon's origins. If this makes it better or worse is largely a matter of personal taste.
* DesignatedHero: King Aspen in Issues 27-28. He claims that the reason Ponyville is being torn up by vines from the forest is because a construction company of ponies and minotaurs are tearing down trees to build an amusement park, and they must replant the forest away from the development site to replace the many animal homes being lost; any pony homes destroyed in the process is simply LaserGuidedKarma. He's not in the right, but you can understand his position... until the final panels show the forest's vines have reached Canterlot, and tied up Celestia and Luna and hung them from a tower. At this point he passes DisproportionateRetribution and straight into self-righteous hypocrisy. The blatant FantasticRacism of the deer as a whole does not help. There's a reason some people interpret him as an ecoterrorist. And it doesn't help that there are comparisons to [[CantArgueWithElves elves]].
* DorkAge: Entered one during the "Reflections" arc ([[BrokenBase where in it is debated]]), it and the stories since have ranged from average to criticized to the point [[FanonDiscontinuity fans reject its existence]]. Note that this was toward the end of Season 4, [[WinBACKTheCrowd which ended the shows own age]] it entered in Season 3, when the comics debuted, making its current shortcomings stand out more.
* DudeNotFunny: While not offensive, many felt the "Reflections" arc fell into this regarding [[https://derpibooru.org/661397 what came of as self ridicule of its faults]], in part because the writers previous works were also funny while being well received.
* EightDeadlyWords: Between the [[CorruptCorporateExecutive purely unlikeable villain]], the Deers hypocrisy squandering what sympathy they had, and the Ponies [[CantArgueWithElves failing to call the latter out]] or do anything useful on their own, many wrote off "Root of the Problem" by part 1. While the finale had [[DeusExMachina significant]] [[IdiotPlot criticisms]], it failed to cause the backlash the writers previous {{Story Arc}}s did, likely because readers had stopped caring one way or another.
* EnsembleDarkhorse:
** While the {{Retcon}} to [[DemonicPossession Nightmare Moons nature]] has been mixed, her latest incarnation, [[spoiler:Nightmare Rarity]], is easily the most popular thing to come out of the comics, impressive given she only appears halfway through her story and is a [[WalkingSpoiler huge spoiler]]. Helping is that she has a [[EvilIsCool cool,]] [[EvilIsSexy attractive]] character design, [[LampshadeHanging is savvy enough to know it]] [[DangerouslyGenreSavvy and pose a serious threat]] despite lacking her [[PhysicalGod previous incarnations power]], and some of the comics most epic and emotional moments came out of her confrontation.
** Luna's pet opossum, Tiberius. Many have called for him to be a character in the actual show.
** Mirror!Sombra was generally well received for having a more developed backstory and being TallDarkAndHandsome.
* EvilIsCool: Bronies seem to really like the idea of [[spoiler:Rarity going evil]] given all the fanart of Nightmare Moon II has gotten.
* EsotericHappyEnding: The 2014 Holiday Special seemed to end happy, but between the HappyEndingOverride it pulled on ''Rainbow Rocks'', FridgeHorror at how fragile Sunset Shimmers forgiveness was, and no evidence that this couldn't happen again, not many readers bought it.
* EvilIsSexy: [[spoiler:Nightmare Rarity]], as nicely detailed [[http://derpiboo.ru/284489 here]] (major spoilers, of course).
** This was even lampshaded in the comic when [[spoiler:[[FanNickname Nightmarity]]]] says at one point, "I'm so hot, I should be on fire!"
* FanficFuel:
** We're given ''just'' enough detail about the MirrorUniverse to get the fanfic authors going.
** The 2014 Holiday Special for the same reasons as ''A Canterlot Wedding'', [[spoiler:criticisms of the The Mane 5 abandoning their friend with little second thought and with [[BrokenBase hotly debated justification]], and their lack of apology afterward.]]
* FanonDiscontinuity: Some fans of the show view the comic as such for its discrepancies in tone, continuity, and characterization. Even those who accept it ([[BroadStrokes or parts of it]]) tend to be dismissive of the following:
** The Reflections Arc for [[TheyWastedAPerfectlyGoodPlot wasting its potential]] MirrorUniverse conflict, [[TheyWastedAPerfectlyGoodCharacter its characters,]] and Celestias [[LoveMakesYouDumb characterization]] (that she ask the Mane 6 to [[LetUsNeverSpeakOfThisAgain never let anypony know that this all took place]] helps).
** The 2014 Holiday Special for details that become questionable when placed alongside ''Rainbow Rocks'' and the human characters [[spoiler:(especially the Cutie Mark Crusaders)]] characterization.
** The "Cattle Rustlers" arc for the massive MoralDissonance and Twilights [[LawfulStupid characterization]].
** "Root of the Problem" for its sheer IdiotPlot and the Deers [[CantArgueWithElves characterization.]][[note]]See a pattern?[[/note]]
* FranchiseOriginalSin: The first story arc cause some BrokenBase over being DarkerAndEdgier, with the next arc [[ContestedSequel getting it worse for being more so]], but were both well received for the same characterizations that made the show popular. Come the "Reflections" arc, by which point the character driven components were largely moved to a dedicated spinoff series, it got criticized for [[BaseBreaker controversial portrayals of major characters]], underutilizing interesting ones, and finishing before it was able to do anything with its potential. Later arcs relied on [[IdiotBall idiotic]] and [[TheScrappy unlikable characterizations]] (like having ''The Princess of Friendship'' do nothing ''while her friends were threatened'') to enable conflict. Note that its LighterAndSofter issues [[ComicBook/MyLittlePonyFriendsForever (including said spinoff)]] have avoided such criticism.
** Issues #15-16 had the [[SeriesContinuityError continuity issue]] of taking place during Season 4 of the show[[note]]Spike mentions the events of [[Recap/MyLittlePonyFriendshipIsMagicS4E6PowerPonies "Power Ponies"]])[[/note]], but reactions to [[RefugeeFromTVLand Daring Do]] seems to ignore that [[Recap/MyLittlePonyFriendshipIsMagicS4E4DaringDont she has been shown by this point]] [[RealAfterAll to be real]]. This could be dismissed as their having other things to deal with thus not effecting the otherwise decent stories reception. Come the 2014 Holiday Special, which takes place after [[WesternAnimation/MyLittlePonyEquestriaGirlsRainbowRocks ''Rainbow Rocks'']][[note]]Sunset using her journal[[/note]], while the [[spoiler:Sunset Shimmer gets subjected to mistrust and hostility that would have made a lot more sense prior, when she was still [[ReformedButRejected proving her reformation]]]]. This time, it's one of the most detested stories for this.
*** It also gets criticized for plot points that were handled better in [[Recap/MyLittlePonyFriendshipIsMagicS2E25ACanterlotWeddingPart1 "A Canterlot]] [[Recap/MyLittlePonyFriendshipIsMagicS2E26ACanterlotWeddingPart2 Wedding"]] ([[spoiler:the Mane 5 abandoning their friend was payed off with an epic villain, action, and they [[JerkassRealization realized their mistake]]]]), and [[Recap/MyLittlePonyFriendshipIsMagicS4E20ForWhomTheSweetieBelleToils "For Whom the Sweetie Belle Toils"]] ([[spoiler:one of the Cutie Mark Crusaders being a GreenEyedMonster, but was potrayed sympathetically enough that her forgiveness received no complaints]]).
* GatewaySeries: There have been reports of people - not just bronies - getting into comics ''period'' thanks to this series. The first issue was one of top 100 best selling comics in 2012. An all-ages comic doing this is good news for the industry!
* HarsherInHindsight:
** [[https://derpiboo.ru/130528 This image]] since the first act!
** Celestia's statement to Twilight in the season 3 finale that Star Swirl "did not understand friendship like you do" comes as rather callous with the reflection arc.
** In the IDW Holiday Special for Equestria Girls, Sunset Shimmer is the victim of cyberbullying. Yeah, [[http://www.dailymail.co.uk/news/article-2877190/Teenage-Little-Pony-fan-posted-heartbreaking-YouTube-video-APOLOGISING-internet-trolls-tormented-days-threw-train.html about that]]...
*** [[Recap/MyLittlePonyFriendshipIsMagicS2E23PonyvilleConfidential "Ponyville Confidential"]] after the above due to the reversal of who got the SympatheticPOV
* HilariousInHindsight: [[http://www.strangekidsclub.com/2012/03/01/check-out-the-sexy-new-superheroine-cast-of-my-little-pony/ This article]], posted before the comic series was announced, showing fanart of the (humanized) Mane Six as pin-up superheroines, mentioning "Somewhere 'bad girl artist' J. Scott Campbell is smiling". Campbell ''did'' do a [[http://1.bp.blogspot.com/-0onesXxyp30/UPhh3un3E-I/AAAAAAABPIA/AHYyvYyHrBc/s1600/image.jpeg variant cover]], with no {{Fanservice}} in sight!
** In ''VideoGame/DiabloIII'', a unique unicorn monster found in [[JokeLevel Whimsyshire]] was named "[[PunnyName Nightmarity]]". [[spoiler:The name isn't used in the comic, but Rarity becomes the second Nightmare Moon]].
** The many "What If [[spoiler: Rarity]] Were Evil?" fan-remixes, ''especially'' [[http://www.youtube.com/watch?v=wtvNZdIwWjc this one]], are all very much HilariousInHindsight now.
** The two Doctor Whooves in #7 is quite prophetic, since the Series/DoctorWho 50th anniversary special had them together some time later.
** Remember the [[Recap/MyLittlePonyFriendshipIsMagicS1E18TheShowStoppers hilariously bad rock performance the CMC performed to try and find their cutie marks?]] Shining Armor's rock ballad in #11 managed to help Vinyl Scratch gain her cutie mark just by watching it!
** The fandom has had a knack for publishing fanart of Rarity battling giant crabs. The cliffhanger to #13 has the Mane Six being attacked by a giant crab, and Rarity in particular seems to be really panicky about it.
*** There was also an [[Blog/AskAPony Ask Blog]] about Pirate Rainbow Dash. Guess which canon pony is the most eager to get her sea legs?
** In chapter #7, Applejack and Rainbow Dash wished that Daring Do was there to rescue them and the others from jail. In season 4, Daring Do is revealed to be real and Rainbow Dash rescues her.
*** Same issue, the Nightmare Forces speculate that Fluttershy would be most susceptible [[CorruptTheCutie to their influence]]. The season 5 opener has the the Mane 6 ''exploit'' her seeming susceptibility to best the BigBad, as if they weren't [[UnderestimatingBadassery underestimating her enough]].
** In issue 17, Celestia and Starswirl travelled to an alternate universe where Dinosaurus still roam and they encountered Fluttershy's Tyrannosaurus Rex counterpart, [[http://fav.me/d65mwj9 this fan comic]] was made a year before issue 17 was released
** Remember Twilight nearly blasting Chrysalis to atoms in the finale of the first four issues? Cue the season four finale where we really see what she can do when she cuts loose.
** Issue #23, the pets-only story, introduces a kelpie that has the ability to command sentient beings with the power of song, though she is apologetic for these actions once the spell is broken. This came out within the month of ''WesternAnimation/MyLittlePonyEquestriaGirlsRainbowRocks'' where the main villains also appear to be kelpies, able to coerce humans to enter into conflict with their siren-like song.
** The portrayal of the deer in "Root of the Problem" is remarkably similar to how they were in the highly popular fanfic ''FanFic/ItsADangerousBusinessGoingOutYourDoor''. And they were just as unpopular there, too.
*** Related to the deer is their role as rulers of the Everfree Forest. People have drawn comparisons to the 4th season premiere where the Forest attacked before, and that episode's own [=HiH=] has comparisons to [[Series/KamenRiderGaim a show airing at the time the episode premiered]]. With this, comparisons to [[spoiler:The Overlords]] can be made.
* HoYay: In issue #25, Rarity is quite taken with Sheriff Tumbleweed's hat, which Applejack quickly points out is the same as hers. Particularly fun is that you can interpret it in two distinct ways: either Rarity is ObliviousToLove from Applejack, or they're together and Applejack suspects her eye is wandering.
* IdiotPlot: "Root of the Problem" would be over in one page, if it ever happened at all, if any of the characters acted intelligent for just a moment. King Aspen could have sent an envoy to meet with Celestia and Luna in person; Celestia and Luna themselves could visit in person; Twilight could have used her powers and authority as Princess. Instead the ponies are completely useless to do anything while the deer jump straight to eco-terrorism without any regard for the chaos they cause. Further, the resolution of the conflict (the deer just invade the construction site and kick Well-To-Do and his workers out) could have been done at the start of it all without the need to attack Ponyville.
* InternetBackdraft: Tedly Anderson caused this in several forums, including IDW's own, with the revelation that he, in the 2014 "Power Ponies"-themed Annual issue canonized dragondicks, a rather polarizing figure in the fandom, known for her vocal criticisms of it, specially men in the fandom. It was aggravated when his defense was that dragondicks' work and political views are just satire.
** Though there were initial claims that IDW had let Anderson go after finishing off two already-in-progress scripts, IDW editor Bobby Curnow has [[http://boards.idwpublishing.com/3/viewtopic.php?f=36&t=12770&start=1650 affirmed]] that Anderson is still on board, considered the situation a large mis-communication, though has instituted a "no OC" policy for future issues to prevent this from happening.
** This has not stopped some fans from avoiding any issue penned by Anderson, or in some cases, to stop buying the comic outright.
** Some have taken the 2014 Holiday EQG written by Anderson, which involves cyberbullying done by a online handle named Anon-a-Miss, as Anderson's TakeThat to the 4chan crowd's reaction to the 2014 Power Ponies Annual and criticism around that. Even though the Holiday issue was already in the works before the Power Ponies annual was out (based on [[https://derpibooru.org/716623 Tony Fleecs' tweeting a work in progress from the issue]]). It didn't help that a majority of the plot was also based around a [[BrokenBase very polarizing]] [[Recap/MyLittlePonyFriendshipIsMagicS2E23PonyvilleConfidential episode]].
* IronWoobie: In main series #21, it's revealed that while Trixie's reputation was already pretty bad after ''[[Recap/MyLittlePonyFriendshipIsMagicS1E6BoastBusters Boast Busters]]'', after ''[[Recap/MyLittlePonyFriendshipIsMagicS3E5MagicDuel Magic Duel]]'' everyone thinks she's evil. Despite this, she is determined to continue performing and prove that she can be a good pony.
** The Citizens of Wuvy-Dovey Land can be considered this. They never lose their happy and loving nature, continuing to be nice people [[spoiler: even ''after'' the changelings destroy their town.]]
* ItsShortSoItSucks: Many feel the real reason the Kelpie got of so absurdly easily in issue #23 is because there wasn't enough pages left in the story to deal with her better. The following issue, while lacking stand out criticism, wasn't long enough to give Discords time-travel shenanigans what fans felt was justice.
* MartyStu: Mirror!Sombra can come off like this. Celestia falls in love with him, Rarity notes how attractive he is and even Fluttershy, who (unlike Rarity) has never shown any romantic interest in anyone before, becomes weak-kneed and heart-eyed from just a single look. He outright refuses and doesn't show any indication of even considering Mirror!Celestia's offer to unite him with his true love, Celestia, because he is too noble. He's kind, affable, charming, and has yet to show any real flaw aside from his relationship with Celestia having a negative impact on his kingdom. The fact that Celestia falls so in love with him that she acts OutOfCharacter to a ridiculous degree doesn't help with that opinion either.
** Considering the state of the Kingdom despite having Mirror!Discord and Mirror!Queen Chrysalis, it looks like he is barely managing against the tyrant sisters.
* MemeticMutation: Several have become part of the fandom's image macro core image set:
** Fluttershy's "Nature is so fascinating" line from Issue #3 has [[http://derpibooru.org/search?utf8=%E2%9C%93&sbq=nature+is+so+fascinating&commit=Go picked up a lot of mileage]]. The circular panel with her has been also used to create "Bad Advice Fluttershy" macros.
** Pinkie's reaction to opening the door with the giant eyeball in #4 (replacing the eyeball with anything else)
** Rainbow Dash's "Two Words!" at the end of #5
** Several reaction shots from the arc of #11-12, including "Cadance laughing at your misery", "Cadance tearing up", "Cadance slyly contemplating", and "Shining trying to say 'Hello'".
** Twilight pointing out why Cassie is EasilyForgiven to Rainbow Dash turned into a rather malicious meme where she tries to justify the actions of various villains akin to "X Did Nothing Wrong".
* OvershadowedByControversy: Bring up the 2014 annual, and all you'll hear about is the entire mess involving the issue's writer and his choice of fan OC to include in the background. This also has applied to any issue following this that Anderson is the writer on, with some readers simply refusing to acknowledge the issue due to Anderson's writing, despite the praise others might give it.
* PanderingToTheBase: The comics are obviously aimed at the older brony fandom than the kid audience the show is intended for. The stories are darker and more mature, as well as featuring elements the fandom loves over the SliceOfLife plots of the show, references to death are not uncommon, and there are many nods to the fans in the background scenery.
* RescuedFromTheScrappyHeap: Angel saves the whole town, which he'll never get any recognition for. We can probably consider his Scrappy moments paid back in full after this.
* RomanticPlotTumor: In the "Reflections" arc. The premise of an alternate universe with evil versions of the cast and good versions of the villains quickly takes a backseat to Celestia's relationship with an alt version of Sombra.
* RootingForTheEmpire: Given all the criticism the Deer received in "Root of the Problem", many readers wound up rooting for the villain, Well-To-Do, if for no other reason then [[ScrewYouElves to screw them over]]. They wonder why the ponies didn't, given the Deer proved no better and they would have gotten an AmusementPark out of the deal otherwise.
* SeasonalRot: Katie Cook's later story arcs haven't been as well received as ''The Return of Queen Chrysalis'' or her SliceOfLife stories. The quality in general seems to have dropped once Heather Nuhfer left to work on other projects.
* TheScrappy:
** ''Twilight Sparkle'', if you can believe it, in ''The Good, The Bad, and The Ponies''. It seems that with the comics' more action-oriented stories, the only way they can think to avoid having Twilight's magic become a StoryBreakerPower or her status as Princess to [[ScrewTheRulesIMakeThem solve any social problem]] is to make her LawfulStupid and arbitrarily refuse to use it because of some rule [[{{Asspull}} the writer just made up]]. Her road to scrappydom began an issue or two earlier with her forgiveness to the Kelpie, which was at least in-character, more then can be said here. Worse, this had an easy, obvious fix of [[DeusExitMachina writing her out of the story like Spike was]], one has to wonder if her presence [[ExecutiveMeddling was forced]].
** Writer Katie Cook has recently become accused of the reason for the declining quality of the comics. While her earlier issues ("The Return of Queen Chrysalis," "Zen and the Art of Gazebo Repair," "Neigh Anything") were well received, her recent work has been "Reflections," "Cattle Rustlers," and "The Root of the Problem," which have generally gotten mixed to negative reception. However one has to keep in mind that in the middle of these, she recently had a child plus is still drawing her own series, ''Webcomic/{{Gronk}}'' (which likewise has recently started publication in comics) and thus likely was not able to focus on her storylines like she used to.
* SnarkBait: The only reason many fans acknowledge the "Cattle Rustlers" and "The Root of the Problem" arcs are for the sake of ridiculing how poorly they turned out, [[FanonDiscontinuity they don't exist to them otherwise]].
* SomeAnvilsNeedToBeDropped: The 2014 Equestria Girls Holiday Special is not exactly subtle about the dangers of cyber-bullying... but that's probably for the best.
* TastesLikeDiabetes: PlayedForLaughs with Wuvy-Dovey Land.
* UglyCute: Jim the Cave Troll. Sure he's a hulking brute who could easily crush a pony if he wanted to, but he's so innocent and carefree it's hard not to see him as anything other than the softie he really is. And he genuinely did love the Mane Six's company.
** The uncorrupted moon bunny in Issue #7. Fluttershy certainly thinks so.
* UncannyValley: Issue #1's [[http://www.amazon.com/Little-Friendship-Magic-Subscription-Variant/dp/B00A8RS4BC/ SUB]] cover by Jill Thompson. The mouths just look wrong.
** The costumes that Pinkie carries around.
%%* UnfortunateImplications: Shining Armor singing a parody of OingoBoingo's "Little Girls", a song about an adult attraction to teenage girls. Thankfully the comic uses the word "mares" instead of "fillies".
* WhatDoYouMeanItsForKids: Its promoted as an all-ages comic, though the series thus far has been a little darker than one would expect from a series where most of the covers feature cute, colorful ponies.
* TheWoobie: Luna on [[https://derpibooru.org/341850 Andy Price's variant of #8]].
** Rarity is very sympathetic in the Nightmares arc, especially when it's revealed that [[spoiler:she has self-esteem issues because she fears that her friends will abandon her because they find her useless. Fortunately, her friends convinced her otherwise at the end.]]
** Spike during [[spoiler: Nightmare Rarity's dream sequence]] at the end of #7.
** Princess Celestia, as a result of the [[spoiler:Sunset Shimmer short]].
*** She's either this or JerkassWoobie in the "Reflection" arc [[spoiler: where she ignore Starswirl's warning to see her lover King Sombra which ultimately causes her to be separated from her mentor then her lover.]]
** Sunset Shimmer in the Holiday Special [[spoiler:where she gets framed for being Anon-a-Miss, a person posting secrets on Mystable, gets rejected by the Humane five and once again becomes the most hated student in Canterlot High. Post-HeelFaceTurn Sunset Shimmer can't catch a break!]]
* TheyWastedAPerfectlyGoodPlot:
** The "Reflections" arc. A lot of fans were really excited at the prospect of getting to see a mirror universe with evil versions of the mane cast and good versions of the bad guys. Unfortunately, the bulk of the arc ended up revolving around [[RomanticPlotTumor Celestia's relationship with alt!Sombra]]. The alternate versions of the Mane Six get very little screentime, leading a lot of readers to feel that the alternate universe premise was wasted even amongst who genuinely liked parts of the arc. This is even directly referenced in the final issue's postscript page, where the alternate Mane Six wonder if they should have been more involved in the story, though some regarded that more as a TakeThatAudience moment.
** "Root of the Problem" could have been a good arc had it focused on the Everfree Forest or the deer. Instead, we get a [[StrawCharacter straw villain]] that could make the villains of ''WesternAnimation/CaptainPlanetAndThePlaneteers'' cringe in embarrassment that still [[DesignatedHero failed to make the Deer the good guys in comparison]], and a conflict [[IdiotPlot that should have been resolved before the ponies got involved.]]
** The Equestria Girls Holiday Special also falls under this, as after ''[[WesternAnimation/MyLittlePonyEquestriaGirlsRainbowRocks Rainbow Rocks]]'' fans were eager for more Sunset Shimmer. We could have had a nice heartwarming character building issue on the backdrop of Christmas/Hearth's Warming Eve. Instead it blows it on a rehash of "Ponyville Confidential" which lacked what left the episode "merely" controversial. [[spoiler:Also, the potential that could have come from Sunset being subjected to the same bullying she subjected others to, looking into how fragile her forgiveness was, or give her friends a JerkassRealization over this, never shows up. By taking place after ''Rainbow Rocks'', the chance to give everyone a justifiable reason for Sunsets treatment (she had yet prove her reformation) and explore why she became so [[ShrinkingViolet emotional venerability]], is likewise wasted.]]