When an application is deployed on PE using the AMX API and not referenced, the Application Server GUI throws errors while displaying that application. AMX requires that you explicitly handle references for your applications. For example, when an application is deployed, the DeployedItemRefConfig needs to be explicitly created. To simplify the deployment process, references are assumed to be present in PE, which in turn causes the issue with Application Server GUI.
Always create the reference to a resource or application after creating it.