same problem after upgrading to iOS 9… can't get rid of the Game Centre notifications… i HATE them!!! 
i have already –
logged out of Game Centre
turned on Restrictions for Multiplayed Games & Adding Friends… (Apple's suggestion…)
turned off Notifications for Game Centre
if i wait for the 12 seconds it takes for the log in screen for Game Centre to come up at the start of Bejeweled to come up and then cancel it, then force close the app, then do it two more times, the fourth time i open Bejeweled, it doesn't ask me to log in, but then later the same day i would have to do it again… (this used to work on iOS 8 and was what Apple started to suggest to me when i rang them…)