Because that's what happens when you incorporate Yaya into this team. It's the same problem Pellegrini has had all season.
Yaya isn't good enough in a 2 man midfield against opposition who will have a fair share of the ball, hence he's played in a 3 - however this means he pushes Silva/KdB out wide as Yaya will be central.
Option 1: 2 man midfield with Yaya = horribly exposed CB's, but places our attacking players in their favoured positions.
Option 2: Yaya in a 3, displacing our best AM's out wide. More solid defensively but weaker & loss of width up top.
Option 3: don't play Yaya & lose some control in midfield but have everyone in favoured positions.
For me in these sorts of games (disregarding fitness issues) I'd still opt for option 3 as we did against PSG - Yaya from the bench if needed. And in games where we're stronger favourites I'd opt for option 1 - hoping the benefits of extra creativity outweigh the defensive issues.