United found themselves behind for the seventh time in 11 games this season, and have now conceded seven goals in four Premier League home games.
And Rooney knows it cannot continue. He said: "Of course it is a concern.
"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."