I had a similar problem, this is because when you install the nuget package, it installs the latest boot download, which is now 3.0, and Twitter.Bootstrap.Mvc4.sample is set to 2.x.
If you do not need 3.0, you can download version 2.x and copy the scripts and contents to the appropriate folders.
For 3.0, moving css files from ~ / Content / bootstrap to ~ / Content.
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