It's a problem.
I don't see Ruben's defensive positioning being good enough on the left or right of that three. He's never been any kind of right or left back to be able to cover one of the wider positions. So if he plays, it's got to be central.
But our build-up play suffers enormously if the defender in the middle of that 3 isn't Stones or Laporte. But Stones is the only one who looks anywhere near comfortable on the right so that's forced Pep's hand a bit.
With Stones injured, I think we have to get Laporte in the starting line-up for his passing ability. Given that's more effective from the middle, and Aké's really nailing down that left-hand side, it seems obvious to play him centrally, and move Akanji out to the right (where he's played occasionally, is a step down from Stones, but is the most obvious option there).
Ruben makes sense as one of two central defenders in a standard back 4. But I'm not sure his passing is what we need in the middle of a back 3.
Aké - Ruben - Akanji is a back 3 that would struggle to bring the ball forward effectively.