One is the difficulty of moving stuff about. If you conclude that the beginning isn't right, you have to use arrows and brackets. Worse if it's not on the same page. And the same when vast scenes have to shift about.
Re-reading an outline can help. It's interesting, however, to plow into the story and then realize that you had an opening scene that separated the heroine from her parents so as to plop her in the thick of things.
Then, fixing that would be simpler if I had started this one on the computer and not longhand. But that would mean more time spent working longhand on outlines in places where the computer is not easily lugged, and so larger piles of never written outlines. Longhand writing tackles that problem two ways.