grunt-uncss creating duplicate selectors

I'm using grunt-uncss to cleanup my css selectors in a bootstrap / angularjs project I'm working on. I'm using the urls option because I need uncss to parse css at runtime since it's an angular app. I'm also using the files option because I can't get uncss to work without it. This is causing some duplicates in my css. Here's my configuration:

uncss: {
  dist: {
    options: {
        urls: ['http://127.0.0.1:8282/build/index.html#/dashboard', 
               'http://127.0.0.1:8282/build/index.html#/servicedesk', 
               'http://127.0.0.1:8282/build/index.html#/email', 
               'http://127.0.0.1:8282/build/index.html#/calendar', 
               'http://127.0.0.1:8282/build/index.html#/customers']
    },
    files: {
      'build/css/raw/tidy.css': ['build/index.html']
    }
  }
}

index.html has two css files, site.css which contains all my application specific selectors and classes, and bootstrap.css

When uncss runs it duplicate many selectors. For example, in site.css there is exactly one

servicedesk {
  display: flex;
  width: 100%;
  height: 100%;
  flex-flow: column nowrap;
  justify-content: flex-start;
  align-items: flex-start;
  align-content: flex-start;
  flex: 1;
  margin: auto;
  padding: 1em;
}

after it runs there are 2. I'm not sure why this happens, but I think it is because it processes twice, once at runtime and once using static files. Not sure how to fix that