Personal opinion here, but I think Pep got the personnel of the starting team messed up, which is why some players just looked out of place:
The Kevin-Gundogan midfield pair was imo a bad idea (I think he did this against Wolves too which was also not great imo), the reason David-Kevin works is because David plays a little higher and plays as the dribbler, short passer, or magician (more of a CAM, think Iniesta) if you will while Kevin plays a little deeper to orchestrate the play (more of a CM, think Xavi). This pairing is better than a David-David or Kevin-Kevin combo because they complement each others strengths and weaknesses. Gundogan is a similar player to Kevin, hence the midfield pairing was like Kevin-Kevin which wasn't perfectly balanced.
The solution is to rest Kevin (which he needs) and play Bernardo-Gundogan as the midfield pair which would mimic David-Kevin. This also puts Bernardo in a much better spot because as most ppl saw he was quite ineffective as a RW, but after substitutions he played centrally and was immediately better suited to the role.
I think Pep knows Bernardo is better centrally, but is playing him out wide because Sane-Sterling are the only options, while the midfield already has 3 players, Bernardo out wide means we have 3 wingers and 3 midfielders. I think Diaz should play out wide though, he's young enough that he isn't drilled to play purely LW or RW and can slot in as both, and he is far more comfortable beating his man than bernardo and has shown excellent finishing ability (which Bernardo hasn't). Diaz is the answer to Pep's winger problems, the sooner he realizes the better, I don't want to wait next season for him to figure this out, like alot of people said about Delph as a LB (or playing Sterling more centrally) last season, Pep, use Diaz as your winger, not Bernardo.