Often we as model builders want to create something perfect. The actual builders were not striving for perfection but for the best product for the lowest price build in the shortest time with the material they had at hand. This means nails, dowels and planks were not perfectly alligned but efficiently drilled and placed, creating in our eyes a kinder garten chaos.
I believe, IMHO this is because the real ship was built by thousands of people, where one group start the task, and another completed. In the case of a model, we are a single entity (for the most part) in control: from start to finish. Also, the size: On the real ship, it is hard to find the blemish unless you look specifically at it. The model is relatively small and you can see everything at glance.We as model builders are often too precise if we compare it with the real thing.