We use coffee-script and emblem for templates in project. Webpack is used for bundling and Karma to run tests. I've tried to use emblem-loader for emblem processing with webpack. Here  is the repository I created with simple example how to reproduce it.
karma webpack config (coffee-script):
webpack:
      module:
          loaders: [
              { test: /\.coffee$/, loader: "coffee-loader" },
              { test: /\.emblem$/, loader: "emblem-loader"}
          ],
      resolve:
        extensions: ["", ".emblem"]
    webpackMiddleware:
      noInfo: true
Template is imported via emblemTemplate = require 'template_path.emblem', then trying to do emblemTemplate(context).
Resulting Errors:
- in PhantomJS: 
Can't find variable: compiled - in Chrome: 
ReferenceError: compiled is not defined 
Definitely the problem is with processing the template and not template itself for loader returns function that check if (!compiled) {...}.