scored two goals but warned Manchester United they must buck up their ideas if they are to challenege for the title this season.
Rooney's salvo, in addition to goals from Robin van Persie and Danny Welbeck, allowed United to record a 4-2 win over Stoke in Saturday's Premier League clash at Old Trafford.
It also took Rooney to 200 club goals - for United and Everton - an early present for his 27th birthday on Wednesday.
However, 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."
In diverting home Charlie Adam's free-kick for the first own goal of his career, Rooney was becoming the first United player to score at both ends since David Beckham at Blackburn in 2001.
Michael Kightly then struck after United had responded with three goals of their own, meaning Rooney's second was required to keep the Red Devils four points adrift of pacesetters Chelsea.
"We keep starting badly," said Sir Alex Ferguson. "Early goal against Fulham. Early goal against Tottenham. Early goal today.
"We are giving ourselves uphill fights. You don't want it to happen and hopefully we will get it sorted.
"The second in particular was a really slack one for us to lose."
Rooney was unaware of his personal milestone until informed after the final whistle.
It was what he was told beforehand that bothered Stoke boss Tony Pulis more.
"I was disappointed to see him on the team sheet," he said. "I thought Alex might have rested him today.
"Wayne is a great player. You watch him at times and his movement is absolutely first-class."
Rooney's partnership with Van Persie looks as though it might pay big dividends over the coming months, with both men equally adept at moving wide and creating a chance for others, as the Dutchman did today.
"We are getting more of an understanding," said Rooney.
"That is the first game we have started together up front and we have both scored. I am sure it will get better."
It was only Stoke's second defeat of the season, not a disastrous statistic considering they have played all the title challengers.
And, whilst Chelsea have a clear advantage at present, Pulis is predicting a thrilling race.
"They have all got players in their teams who can change games," he said.
"Manchester United have leg-beaters. They can beat you with a pass or with movement.
"That is what great teams have, all mixed up into one.
"Manchester United have got it, Chelsea, Arsenal. It will be a great Premier League this season.
"Tottenham got beaten today but they have got some outstanding players and obviously you have Manchester City in there."