OS X restarts every app when waking up
I presume you're talking about Resume, a feature that will cause apps that were left open when you logged out to open again when you login.

From your explanation, I presume you see a window of an app, but then it will fade out and appear to 'restart' — in actuality the app hasn't loaded once yet, and is loading, not restarting.

You can stop Resume by unchecking the Reopen windows when logging back in option in a log out or shutdown dialog.