It was the seventh time in 11 matches in 2012-13 that Sir Alex Ferguson's side had fallen behind and they have now conceded seven goals in four league home matches.
"Of course it is a concern," Rooney is quoted as saying by The Daily Mail.
"We can't keep doing that. No disrespect to Stoke, but better opposition will punish us. We need to keep working and keep defending well.
"Hopefully soon we will get the players back who can provide a bit of cover for us because if we want to be successful this season, we can't keep doing that."
United remain four points behind Chelsea in second place in the league table.