In the "Teleportation" chapter of Choice, despite trying everything to get the Elements of Harmony to work, Twilight fails to realize the obvious reason why — they aren't working because the remaining bearers’ friendship is fraying from the stress of the war and Fluttershy's defection. At this point, Equestria is losing the pony-human war to the point where they are trying to use the Elements’ power to teleport to another world. The ponies have already lost so much and are desperately trying to hold on to what little they have left. Twilight is doing the same; until now, the Mane Six’s friendship has always been something she could rely on, even in their darkest times. She can’t bring herself to face the Awful Truth that even their once-unbreakable friendship is falling apart.
Adding on to that, there's also the fact that out of all the Bearers, Fluttershy was the only one to live up to her Element by rejecting the madness and defecting to aid humanity. Applejack resorted to dishonest methods to keep her farm afloat, Rarity never acted on her own apprehension about the war for self-centered reasons, Pinkie Pie has become a Stepford Smiler and continues to be on the side of those bringing suffering instead of happiness (on top of not acting on her own doubts about the war), Rainbow Dash just became completely blindly loyal to Celestia without realizing or caring about the atrocities Equestria was committing, and Twilight failed to take the lessons she'd learned about the magic of friendship into account while dealing with the humans.
In the "Divine Justice" ending of Fallen, Harmony magically transforms all the Newfoals back into humans. Why couldn't it leave that up to Twilight to give her a chance to atone for her mistakes, like she did in Rest? Because Discord is dead in Fallen and his blood is/was an essential component of the Newfoal-to-human cure.
In the "Harmony's Chosen" ending of Fallen, all of the Mane Six except Fluttershy are put on trial. During Applejack's trial, it is revealed that every single pony she sold out to the ESS died in the labor camps. It is possible that the ESS treated those ponies even more harshly than most prisoners because it was Applejack — a national hero to Equestria and the Element of Honesty — who sold them out. The entire country, including the Equestrian government and the ESS, held absolute, unquestioning faith in their princesses and heroes during the entirety of the Conversion War. They would never consider that the Element of Honesty's bearer would lie about somepony being disloyal, just to get a few more bits in the bank to save her family's farm...and from their perspective, anypony who was bad enough to be reported on by the Element of Honesty herself must have been a very bad pony indeed.
