Basically there were a lot of lawsuits going back and forth in the pre-production that ultimately resulted in Guillermo Del Toro leaving the as director after nearly two years of planning and developing the films according to his vision. Then Peter Jackson had to step in as director with minimal preparation time and he essentially winged the whole thing. It was originally planned as two films but was expanded to three at the last minute. They were also using all sorts of cutting edge technology in the filming process and the sheer scale of the films would have been daunting enough even with adequate time to prepare.

As per Jackson

Because Guillermo del Toro had to leave and I jumped in and took over, we didn’t wind the clock back a year and a half and give me a year and a half prep to design the movie, which was different to what he was doing. It was impossible, and as a result of it being impossible I just started shooting the movie with most of it not prepped at all. You’re going on to a set and you’re winging it, you’ve got these massively complicated scenes, no storyboards and you’re making it up there and then on the spot. I spent most of The Hobbit feeling like I was not on top of it. Even from a script point of view, Fran [Walsh], Philippa [Boyens] and I hadn’t got the entire scripts written to our satisfaction, so that was a very high pressure situation

You can read a slightly more detailed explanation in the wikipedia article.