For me one of the most difficult parts was getting the ordering of the various loaders right and understanding what each loader does exactly. I'm still not sure what the css-loader does specifically compared to the style-loader and what css-loader/locals does differently, I just understand which one I need to use in each configuration.
This one confusion probably gave me the biggest difficulties when I initially tried to wrap my head around all of webpack and hot reloading to replace my existing browserify-based setup. Most tutorials seem to be written for either complete beginners who haven't previously used any transformations/loaders at all, or people who already fully understand how webpack works. There doesn't seem to be much content addressing intermediate users who want to convert real-world code bases to webpack.