Sneha, are you able to elaborate a little bit re: what exact setup you mean by "Shared Server"?
Is your Java or .NET application hosted on the same machine as where you've installed the AppDynamics Controller? If so, please be aware that kinda setup is known to cause problems. The Controller is a very resource(I/O and memory) intensive component. Now your application (depending on usage, concurrency and level of application complexity) could be equally resource intensive as well. Trying to cram these onto an infrastructure that is not sized for such an operation will lead to resource contention and resulting problems, like you suggest. If this is a Production type setup, then strong suggestion is to have a separate infrastructure for hosting the Appdynamics Controller (and other backend server software such as End User Monitoring Processor and Events Services).
Please note that our agent software(which typically resides within the context of your application) is highly optimized for extremely low overhead and almost never is the reason for an application performance bottleneck(on the application it is monitoring in the first place). Hope that helps