I had the same problem and a little search led me to the following page:
http://forums.asp.net/t/1586914.aspx?Unable+to+edit+CSS+file+
In short: add a fake parameter to the end of your CDN URL to get rid of your errors. It also makes intellisense work correctly.
Example:
<link href="//maxcdn.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css?parameter=1" rel="stylesheet">
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