I have two theories on the Darkshore events contradicting each other.
1. Blizz is purposely doing that to mess with us and will change things on prepatch release to make more sense. They mentioned they were planning something cool story-wise, so I could see it being this. Only issue is whether this could cause a lot of bugs in the game with such a change.
2. The old gods are toying with the Alliance and Horde. Our perceptions of the events are skewed on both sides due to old god influence. This would work in their favor to pit us against each other in order to weaken both sides.