Probably the most obvious screw-up is the timetravel/alternate timeline plot. It’s as though Blizzard wanted to do timetravel, realized the clustercluck of paradoxes that would follow, and then just called it an alternate timeline on top of it. But then they felt they needed to canonize that alternate timeline by giving us the main timeline’s Legion, which they then had to justify by saying that the Legion exists somehow in the multiverse. That creates its own string of story concerns.
Next is how it undermined the conclusion of MoP. Why would Vol’jin brew conflict back with the Alliance? This was right after Varian looked him in the eye and chose not to dismantle the Horde for the sake of peace. MoP could’ve been the perfect climax to the Horde and Alliance conflict; where our characters would’ve learned the lessons of Pandaria and now had to teach them to our own people who weren’t there and are still trapped within the cycle of hatred.
Last, and certainly not least, WoD was the point where the player character became the undisputed main character of the story. Prior to that, we were at most pretty important to the moving of events, and at least we were witnesses to the story. The story kinda shifted between those ranges, because yeah we did battle the likes of the Lich King, but we usually did so as adventurers banding together, not as a main character and his helpers. WoD was when NPCs started kissing our butts, especially at our Garrison. This created a vicious cycle where we were given main character plot lines, which begetted more main character treatment, which begetted more main character plot lines. All of a sudden we’re not one of many heroes of Azeroth, we’re now THE hero of Azeroth. We live in an internalized story where we are superior to other players, and in their perspective they are superior to us.
Anyway, I’m sure there’s more things in WoD that were not just bad story telling but were damaging to the story moving forward, but that’s all I can think of at the moment.
WoD is literally a cursed expansion.