I have just tested this and in my tests this doesn't happen. Calling the app.exitApp() should be destroying all object instances. The app appears to be left in the background, but in fact is closed. Can you elaborate more on how you found out that it creates multiple Kendo UI app instances? Is there a problem that comes out of this? If you can provide a sample app along with steps to reproduce your problem, I could better address your problem.
I'm looking forward to your reply.