Bayer won 2-0 at the Etihad on Tuesday night thanks to goals from Alejandro Grimaldo and Patrik Schick.
Stones said afterwards, “Lots of things (were missing). You can dissect and look at it in so many different angles. I think all in all, we didn’t have that edge to us, the clinical edge, the aggressive edge, and we lacked in quite a few things which is very uncharacteristic for us as a team and players.
“We’re all disappointed, I’m disappointed to have led the team out tonight and it to finish that way, from trying our best to break them down and working on it in training, we knew they were such a good team in possession and found it difficult at times to keep them in one area of the pitch and they got out.
“There were a lot of good things but it’s a night we need to reflect on massively.”
The result was a first defeat in the Champions League group phase since 2018.
“Not good,” Stones replied when asked about the mood in the home dressing room. “It’s a difficult one to summarise really. A lot of emotion, I think it’s going to have to be one we have to look back at.
“I think we weren’t good enough as a collective, created a lot of chances (and) we could be stood here, it could be 4 or 5-2.”