Cameras appeared to show Branislav Ivanovic holding his neck after seemingly being hit by an object thrown from the stands following Cesc Fabregas' 88th-minute winner on Sunday.
But Mourinho believes the game was played in the right spirit.
"The game was correct," he said. "Correct on the pitch, correct in the stands and hopefully correct outside.
"It is not easy, because emotionally it's a big game for them and a big game for us.
"The referee [Andre Marriner] also helped because he is a very stable man who didn't create problems for the game, he solved them.
"But I think both teams deserved credit because, in a very emotional game, they were very correct.
"If in the end of the game somebody threw a pound, put the pound in your pocket and go. If it is chocolate, eat it. No problem."
Asked whether his players needed a pound, Mourinho responded: "Everybody needs a pound. Never throw a pound away."
Mourinho also revealed the injury that ruled Loic Remy out of Sunday's fixture was minor and that he expected the striker to be available for next weekend's clash with Manchester United.
