The Blues boss feels the striker's unhappiness at the club stems from when his manager announced he was behind Robin van Persie in the pecking order at Old Trafford
The England international has been the subject of two failed bids by the Blues, with the west Londoners expected to submit another offer after the two clubs’ clash at Old Trafford on Monday.
Speaking ahead of the game, Mourinho was warned he could receive a heated reception from the United crowd, due to his interest in Rooney, to which he told reporters: "They are against me?
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"We are trying to get a player that a manager told 'You will be a second option' for him. We are not going for Van Persie. They don't have to be against me. If I say Ramires is a second option for me and he plays when Lampard is tired or injured, if someone comes here to get Ramires, nobody is upset."
When subsequently asked to clarify if he felt that was Moyes’ fault, Mourinho replied: "Of course."
However, the former Real Madrid coach did admit that keeping star players happy in a big squad can be difficult.
"In every big team, I am not criticising, you have first options and second options, and those second options must be very good players," he added.
"Of course big teams must have second choices. Big players too. The point is if the players are happy to accept that situation."
Moyes has insisted Rooney has a good chance of facing Chelsea on Monday, despite being left on the bench for their opener against Swansea, which did not surprise Mourinho.
"It means they have a fantastic squad," he said. "Fantastic. I was playing against them last year [with Real Madrid].
“He was on the bench and he [Ferguson] was playing Van Persie, [Danny] Welbeck, [Shinji] Kagawa. The squad is amazing. So it is natural that some players have to be second-choice.”