By default, ASP.Net bundler is looking for non-minified files (without .min in file name). If you have included script files with .min - they will not loads with build.
If you strongly wants to include minified files, just rename them from script.min.js to script-min.js, for example.
Also, the reason of not-working scripts could be some bundling errors. In this case, you can try to the end of BundleConfig.cs next row: bundles.IgnoreList.Clear();.