In my ASP.NET MVC3 project there are two (2) web.config files. One is the global configuration at the root of the web project (/web.config) and the other is on the Views folder (/Content/Views/web.config).

My NuGet package needed to transform both files. In the root web.config it added an entry in <appSettings> and that worked fine. On the Views web.config it had to add a namespace entry in the razor web pages section so that this namespace was available in all views.

The problem is that when even though the .transform files are in their proper directories, NuGet performed the transformation of the Views/web.config on the root web.config, in other words, rather than merging it on the existing Views/web.config it added the section in the root web.config thus causing errors.