Pep obviously had been told that Stoke away would be tricky, I just dont think he realised that Stoke at home could also be tricky. Or Boro/Southampton/Everton.
My guess with Kompany is that before all of his recent comebacks the manager was told by the medics that he was fully fit, or as fully fit as he ever was going to be. And then he broke down, either during a match or in training. Its Catch 22 now. Pep isnt going to believe he's injury free until he's played a run of games without picking up an injury and he isnt going to get a run of games because Pep doesn't trust his fitness.