Ferguson is not believed to be upset with Capello, but the workload may cost him his most prolific striker at Wolves tomorrow, when an obvious replacement in Michael Owen has just been ruled out for the season.
"We didn't speak to England to ensure he wouldn't play the full game but there were some changes made and I thought Rooney would have been one of them, particularly as he went into the game with a small injury," said Ferguson.
"It is disappointing.
"When you are playing on that pitch for almost an hour on Sunday and then nearly a full game on Wednesday it's far too much.
"Now he is a doubt for Wolves."