ScriptManager is not aware of the bundled scripts registered with Bundle Transformer and it emits its original scripts.
Here is a demo where I replicate the issue.
https://github.com/adrianiftode/BundleTransformerScriptManagerIssue
Comments: Hello, Adrian! Scripts and styles are registered in bundles at the level of the [System.Web.Optimization](http://aspnetoptimization.codeplex.com/). ScriptManager has no relation to the System.Web.Optimization and Bundle Transformer. Moreover, this code will cause a error in release mode: ``` using BundleTransformer.Core.Builders; using BundleTransformer.Core.Bundles; using BundleTransformer.Core.Orderers; using BundleTransformer.Core.Transformers; using System.Web.Optimization; namespace BundleTransfomerScriptManager { public class BundleConfig { // For more information on Bundling, visit http://go.microsoft.com/fwlink/?LinkID=303951 public static void RegisterBundles(BundleCollection bundles) { var builder = new NullBuilder(); var styleTransformer = new StyleTransformer(); var scriptTransformer = new ScriptTransformer(); var orderer = new NullOrderer(); var webFormsJS = new CustomScriptBundle("~/bundles/WebFormsJs") .Include("~/Scripts/WebForms/WebForms.js", "~/Scripts/WebForms/WebUIValidation.js", "~/Scripts/WebForms/MenuStandards.js", "~/Scripts/WebForms/Focus.js", "~/Scripts/WebForms/GridView.js", "~/Scripts/WebForms/DetailsView.js", "~/Scripts/WebForms/TreeView.js", "~/Scripts/WebForms/WebParts.js") ; webFormsJS.Builder = builder; webFormsJS.Orderer = orderer; webFormsJS.Transforms.Add(scriptTransformer); bundles.Add(webFormsJS); } } } ``` To fix this error you need to remove the following line of code: ``` webFormsJS.Transforms.Add(scriptTransformer); ``` Because cannot use the `ScriptTransformer` and `CustomScriptBundle` classes together. I recommend to you carefully read the [documentation](https://bundletransformer.codeplex.com/documentation). Start with Rick Anderson's article [“Adding Bundling and Minification to Web Forms”](https://blogs.msdn.microsoft.com/rickandy/2012/08/14/adding-bundling-and-minification-to-web-forms/).