With Visual Studio 2015 I found the problem was caused by referencing the .min version of a javascript file in the BundleConfig when debug=true is set in the web.config.
For example, with jquery specifying the following in BundleConfig:
bundles.Add(new ScriptBundle("~/bundles/jquery").Include("~/Scripts/jquery-{version}.min.js"));
resulted in the jquery not loading correctly at all when debug=true was set in the web.config.
Referencing the un-minified version:
bundles.Add(new ScriptBundle("~/bundles/jquery").Include("~/Scripts/jquery-{version}.js"));
corrects the problem.
Setting debug=false also corrects the problem, but of course that is not exactly helpful.
It is also worth noting that while some minified javascript files loaded correctly and others did not. I ended up removing all minified javascript files in favor of VS handling minification for me.