Rooney made sure of United's progression to the quarter-finals with a late penalty after Ander Herrera and Marouane Fellaini had cancelled out Scott Laird's opener - although the England international sparked debate over whether he dived to win the spot-kick.
With Stuckmann hurtling out of his goal, Rooney hurdled the goalkeeper's challenge before going to ground, with the German left in no doubt as to whether it should have been a penalty.
"After the game Rooney told me: 'Sorry, it was my chance to get a penalty. I had to use that'," Stuckmann told The Sun.
"I say it clear: That was no penalty. I also believe that if the situation had happened the other way around, one of our strikers against the United keeper, the ref wouldn't have given the penalty.
"I have no doubt about that."
United will face Arsenal at Old Trafford in the last eight of the FA Cup.
