I don't ever recall hearing that they gained control of the plane. My impression always was that they caused enough of a disturbance so as to cause the plane to crash. So I guess I'm behind on this one, because what is said to have happened in the article is exactly what I thought happened.
But you never told us what that "other reason" might be.
Poor flying skills on the part of the hijacker who was flying the aircraft.
There's been lots of speculation about whether the plane was shot down, but I'm quite certain that was not the case.