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.
YMMV: A Hollow In Equestria
Alternate Character Interpretation: Diamond Tiara and Silver Spoon. They're portrayed as well meaning in nature, but their approach to caring involved a drill sergeant approach to others, riling them up in an effort to make them succeed at what they try to do.
Base Breaker: The coverage of the Mare Do Well event is this to the readers. Either Rainbow Dash is correct in being angry at her friends for their betrayal, or she's incredibly dense and selfish for not seeing that they were going to desperate lengths to try and help her when she didn't know she needed help.
Breather Boss: The dragon appears to serve this purpose as far as Ulquiorra is concerned.
Cry for the Devil: Chrysalis. Just Chrysalis. What started off as being a stereotypical villain plot, somehow morphed into being a desperate attempt at saving her people/species from extinction, and everything going horribly, horribly wrong.
Godzilla Threshold: Crossed with extreme prejudice. Celestia has taken the threat to Equestria so seriously, she's asked Ulquiorra to go back to his old ways.
Nightmare Fuel: While as Nightmare Moon, Luna was still fully conscious of what was going on around her, able to observe and see everything Nightmare Moon was doing with her body, and unable to stop it. She had to watch as the entity possessing her body killed and ate foals.
The audience being lead to believe that Fluttershy was being murdered, when in reality it was a changeling in disguise.
Oh Crap: The reader's reaction to the ending paragraph of Chapter 58.
Paranoia Fuel: Surprisingly Ulquiorra embodies this trope rather than the ponies. He believes that there's something sinister loose in Equestria, out to kill the Mane Six.
Ulquiorra's actions with ending Cupid's suffering may very well qualify, as he explains how simply waiting for nature to take its course would be extremely cruel.
Ulqiorra's interactions with the CMC in chapter 51 would also qualify. It starts with him stopping Sweetie Belle from crashing into the ground, and eventually ends with him giving Scootaloo some advice on how she may increase her chances of learning to fly.
Teeth-Clenched Teamwork: Anytime Ulquiorra has to work with the mane six on anything of genuine importance, like the safety of Equestria. He has little tolerance for their emotional nonsense, and they abhor his utter brutality and straightforward approach to facing a threat. And that's just when things are in the nonlethal category.
Diamond Tiara and Silver Spoon having to work alongside the Cutie Mark Crusaders would certainly count as well.