If your project has multiple main class entry points and you run bundle:dist, the packaging will silently not create the run script inside of the bundle. When you load then run a bundle on ConductR it will fail with a "No such file or directory" error looking for the file <project-name>/bin/<project-name>.
When you run a project in sbt that has multiple main classes, you are asked to choose which one you'd like to use. I think it would be preferable to either offer a choice or just fail to bundle.