I've noticed that some hotels do collect surcharges when using Stay Plus. From the top of my head I remember the Amarterra MGallery in Bali does. Best course of action is to weigh the value of using your certificate in one of these places, or to select another property that does not levy any surcharge.

Also, I think neither the night stay (using Stay Plus) nor the surcharge will be credited to your Accor account, so better keep that in mind.