Oooof, so many to choose from.

Final Fantasy 8. Final Fantasy 9. Xenoblade Chronicles. Those are the first that come to mind.

They all did the same annoying "and it turns out it was all because of THIS other thing that you've never heard of." (generally known as deus ex machina I believe). It was especially annoying in FF9 and Xenoblade Chronicles because those were stories I really loved, up until the ending.
They did both sorta redeem themselves with nice ending sequences though.