Publishing web project does not include libraries that are referenced by libraries referenced by web project.
Web Project -> ProjectA (class library) -> DependencyForProjectA
Publishing Web Project would not include DependencyForProjectA _if_ ProjectA does not make any use of types found in DependencyForProjectA directly. Thought they might be used via reflection or IoC containers.
This bug report is duplicate of already closed bug report https://connect.microsoft.com/VisualStudio/feedback/details/637071/publish-web-feature-not-including-all-dlls
More developers having this issue http://stackoverflow.com/questions/2815616/visual-studio-2010-publish-web-feature-not-including-all-dlls