Sane injured. Laporte injured. De Bruyne injured. Stones injured. Mendy injured (although not much of a loss since he always is).
I'd say that those are more of a significant factor than the fact that some players are a bit older. That means that rather than being in his preferred position, Fernandinho is having to fill in alongside probably the weakest of our senior CBs. And we all saw how we suffered last season when Fern was injured. Rodri's looked great, but there's always the possibility of a lack of understanding leading to goals when a new player comes in in such an important position.
Having said that, Silva has looked more like the Silva from the second half of last season than the first (when people were tipping him to be player of the season). I also find the reluctance to player Bernardo in CM bizarre, given how amazing he was there last year. If you're going to play Silva, then you need an energetic player to complement him, and that's De Bruyne, Bernardo or Foden, not Gundogan.