Why is a powerful question. It has the power to add depth to a story, but it can also yank the reader right out of it. Just take a look at the Avengers movie for an example of this.
During the story, Bruce Banner loses control and becomes the Hulk. He goes on a rampage, attempts to kill Black Widow, and shows us he's got no control over that side of himself. Yet later, when they have to fight the aliens called out by Loki, we see Bruce transform at will, and he's suddenly able to control Hulk.
Bad storytelling. We never see what brings this change on, so we have nothing to speculate. We can only assume the drop made him land on his had, giving him some insight he wouldn't normally have. Hard to say. But in any case the only answer one can gather is it happened because the story demanded it.
Fixing the issue in your own story can range from simple to impossible. The first step is identifying the issue. Once you do that, you just have to develop something that makes sense.
Good "why"moments have to draw the reader in. These are often most used in mystery novels. So I'd like to start a little discussion. What are the best "why" moments you've ever seen, and why do you think they work so well?