The Umbrella Corporation wrote:
What established lore in Star Trek did it contradict?
"Mudd's Women" established that (di)lithium crystals channel ship's power, while "The Naked Time" established that matter-antimatter reactions are the source of the ship's power. Virtually all later Trek has followed these principles. But "The Alternative Factor" claimed that dilithium was itself the ship's power source and that a matter-antimatter reaction would destroy the entire universe.
But I believe the contradictions mentioned above were those within the episode itself. Sometimes the dimensional shift is felt across the universe, but at other times it happens without anyone noticing. Sometimes Lazarus has to be at the rift site on the planet surface to switch with his other self, but sometimes it happens on the ship.