As a general point, I'd say that playing the way the first team have is really, really difficult. If it wasn't, then everyone would do it. So I'm truly not surprised that with so many changes City struggled to replicate that. And when it isn't perfect, it looks dysfunctional. That's exactly how I'd expect most teams to look if they had a crack at playing the same way. It's taken a fair while for the first team to get that nearly right, and Guardiola isn't totally happy with them and keeps saying they need to improve.
City are playing in a very complicated, demanding manner. They won't get it right all the time even with the first choice players. I'm just not going to beat them up for being a bit off in a game like this. It happens.