Nightmare Moon wasn't the fool shown in the show. In fact, the show never happened. Shortly after defeating Tirek, Twilight woke up in a prison, with a Diamond Dog doing his level best to either annoy her or get her out. She isn't quite sure yet.

Frisk killed everyone, except Sans. Sans eventually managed to destroy them, completely and utterly, using their soul to finally break the barrier. Yet he had nothing. Now, he has a roommate. Sunset Shimmer.

The Elements of Harmony are far from the force everyone thought they were. When Nightmare Moon was defeated and the Elements bound to their bearers, consequences no one could have seen come about. Now, Spike has to deal with it, but doesn't like it.