bar.js

define(function (require) {
  require('hbs!./template');
});

bower.json

{
  "name": "require-handlebars-plugin-bug",
  "dependencies": {
    "requirejs": "2.1.15",
    "require-handlebars-plugin": "0.11.1"
  }
}

config.js

({
  paths: {
    hbs: 'bower_components/require-handlebars-plugin/hbs'
  },
  dir: 'build',
  removeCombined: true,
  modules: [
    {
      name: 'foo',
      exclude: [ 'bar' ]
    },
    {
      name: 'bar'
    }
  ]
})

foo.js

define(function (require) {
  require('bar');
});

template.hbs

<div></div>