I had this issue with an MVC project and here is how I fixed it.
Find :
bundles.Add(new ScriptBundle("~/bundles/bootstrap").Include("~/Scripts/bootstrap.js"));
Change to:
bundles.Add(new ScriptBundle("~/bundles/bootstrap").Include("~/Scripts/bootstrap.bundle.min.js"));
This will set the bundle file to load. It is already in the correct order. You just have to make sure that you are rendering this bundle in your view.