Proc-folder: App generated almost a thousand sub-folders
/proc is very special in that it is also a virtual filesystem. It's
  sometimes referred to as a process information pseudo-file system. It
  doesn't contain 'real' files but runtime system information (e.g.
  system memory, devices mounted, hardware configuration, etc). source


Therefore the directories and folders you observe just represent the processes started by the app. If you see them that the app has still running processes. Some apps contain ant-reverse-engineering technologies by using multiple processes for monitoring each other. Also the Android system may start multiple smaller processes for one app e.g. for background service(s). 

Conclusion: The proc file system is nothing you should worry about. Just ignore it.