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: The Conversion Bureau Not Alone
Author Tract: Written to set right perceived issues with certain other TCB stories. Whether or not certain story plot points are established by fiat, have or lack substance and make sense are things that have divided the readership.
Fridge Brilliance: Why is it the Elements of Harmony aren't able to ponify all of humanity, or do anything else against them? Think about it, the Elements are stated to draw on the Harmony between six special ponies, thus it stands to reason that if it were used on multiple individuals, it would have to overcome the Harmony between those in order to work. And thanks to the war, all of humanity is united against Equestria. Essentially, six souls against SEVEN BILLION. No wonder it wouldn't have worked.
Or it could simply be because what they were trying to do wasn't particularly harmonious.