The club confirmed before the match that Ronaldo was out with a hip flexor problem, leaving Ralf Rangnick to put his faith in Bruno Fernandes and Paul Pogba as central strikers at the Etihad.
However, Keane questioned thar explanation and believes there could be a deeper issue, with rumours in recent weeks of problems in the United dressing room.
“‘I just don’t like it when the manager talks about this hip flexor, I don’t get it,” Keane said.
“We talk about Ronaldo being almost some sort of machine, he’s very rarely injured and then every now and again he comes out with something like that and says hip flexor. It doesn’t add up to me.”
Rangnick was asked after the match whether Ronaldo and Edinson Cavani would make a quick return to the side, but the interim boss was unable to provide any further information on the situation.
He said: “I don’t know. I was hoping to have them available for this game but they weren’t, so I don’t know. We’ll have to wait and see.
“We have two important games coming up against Spurs and Atletico and we have to put our full focus on that.”