The pair have been at loggerheads since Rooney was fined and dropped for the Premier League match against Blackburn on New Year's Eve after a poor training session following an evening out.
And Ferguson offered no sign of reconciliation after Rooney missed a penalty, his third miss from six spot kicks this season, in the 3-0 victory over Bolton on Saturday.
"Wayne had his moments but he can do better," Ferguson said. "I think missing the penalty kick maybe upset him a little bit. But it's a good punishment."