Rooney was on the Stick to Football podcast with the likes of Gary Neville and Roy Keane.
He spoke about United boss Erik ten Hag's decision to take off Marcus Rashford at half-time of their 3-3 draw with FC Porto recently.
Speaking on Stick to Football, Plymouth boss Rooney said: “Some of the changes he is making... You never see top teams changing their centre-backs during the game - or the back four - and that happens on a regular basis.
'The Rashford one... That was the best I've seen him play (v Porto) for a long time and to take him off at half-time and say we've got another game at the weekend is crazy.
“I guarantee on this international break you see videos of him training with a coach away from the training ground - so if he can't do two games in a week, he should have been resting.”