It's not just Greninja. My Lucario has Bone Rush and it won't work, bringing up a long error message sometimes. The same as Xander's here. Water Shuriken doesn't work, Bone Rush, Fury Swipes, anything multi-hit fails to work. Very occasionally, after it kicks me out of the game for trying to use one of the moves, which doesn't happen often, it let's the move work once I get back in. However, this stops working after either a period of time or when I close out of the game and go back in.