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.
Broken Base: Issue #8. Several fans felt that Inkwell ended up stealing Celestia's spotlight in her own issue, while others felt that there was still enough time and character dedicated to Celestia to still be considered in the issue's spotlight.
Fans often disagree on whether certain issues were any good or not. Only the Rarity and Luna stories get universal praise, though plenty of fans enjoy all ten issues.
"Funny Aneurysm" Moment: Fluttershy is worried about anyone finding about her secret chamber in her micro-issue. Normally, this would be a funny joke, but considering the fan-made animation, SHED.MOV, this can border on creepy.
Older Than They Think: Ponyacci is clearly based, in costume if little else, on the commedia character Pagliacci from the eponymous Italian opera. Didn't stop most fans from saying it was a reference to Watchmen.
Recycled Script: Both Twilight and Pinkie's issue involve the heroin meeting her retired idol then give him the will to pursue their career.
Shipping Goggles: Rarity's issue. Among the many things Rarity brought with her to the farm are framed photos of her family, Spike... and Applejack (sporting an unusually coy expression, no less). Cue fans declaring "Rarijack is canon?!", much to the authors' utter confusion, as they were unaware of the fandom's fascination with shipping.